bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 3eeed328e39..7fc030f2870 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -1603,31 +1603,31 @@ <li><b>BRCA Variants</b> - <br> Shows single nucleotide variants (SNVs) and small insertion/deletion variants of < 50 nucleotides (indels)</li> <li><b>BRCA Structural Variants</b> - <br> Shows variants <= 50 nucleotides</li> <li><b>ACMG Popfreq Variants</b> - <br> Shows the provisionally-assigned ACMG evidence code for the Population Frequency group, for variants of < 50 nucleotides</li> <li><b>ACMG Popfreq SVs</b> - <br> Shows the provisionally-assigned ACMG evidence code for the Population Frequency group, for variants of <= 50 nucleotides</li> </ul> </ul> <p> -The <a href="/cgi-bin/hgTracks?genome=hg38&position=default&hubUrl=https://hgdownload.soe.ucsc.edu/hubs/enigma/hub.txt" +The <a href="/cgi-bin/hgTracks?genome=hg38&position=default&hubUrl=https://hgdownload.gi.ucsc.edu/hubs/enigma/hub.txt" target="blank"><b>ENIGMA BRCA1/BRCA2 specs 1.1.0</b></a> track hub contains data from the <a href="https://enigmaconsortium.org/" target="_blank">ClinGen ENIGMA BRCA1 and BRCA2 Expert Panel Specifications</a> to the ACMG/AMP Variant Interpretation Guidelines for BRCA1/BRCA1 Version 1.1.0. The ENIGMA VCEP has adapted the ACMG-AMP codes for the BRCA1 and BRCA2 genes. Before using the data, always verify that the ClinGen Criteria Specification (CSpec) version numbers here match the latest version on the <a target="_blank" href="https://cspec.genome.network/cspec/ui/svi/affiliation/50087"> CSpec Registry</a>. </p> <ul> Data is available for the hg19 and hg38 genomes assemblies and the tracks available are: <ul> <li><b>BRCA1/BRCA2 protein domains 1.1.0</b> -<br> Shows the (potentially) clinically important functional domains for @@ -3526,35 +3526,35 @@ <a name="013023"></a> <h2>Jan. 30, 2023 Addition of GRCh38 patch 14 sequences to hg38</h2> <p> We are pleased to announce the addition of GRCh38 patch release 14 to the <a href="/cgi-bin/hgGateway?db=hg38">hg38</a> assembly. hg38 has been updated with patches since its release in 2013. The GRC patch releases do not change any previously existing sequences; they simply add new sequences for fix patches or alternate haplotypes that correspond to specific regions of the main chromosome sequences. For most users, the patches are unlikely to make a difference and may complicate the analysis as they introduce more duplication.</p> <p> More information on how patch sequences are incorporated can be found on the <a href="https://genome-blog.gi.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. The blog post contains details about the new -<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/latest/" +<a href="https://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/latest/" target="_blank">/latest</a>, -<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/initial/" +<a href="https://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/initial/" target="_blank">/initial</a>, and -<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/p14/" target="_blank">/p14</a> +<a href="https://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/p14/" target="_blank">/p14</a> download directories on the downloads server. With the addition of new sequences to hg38, we can expect to see BLAT return more matches to the genome.</p> <ul> <li> The <b>initial/</b> subdirectory contains files for the initial release of GRCh38, which has 455 sequences, 261 alternate sequences, and no fix sequences. It is the same as the parent download directory. This is probably the best genome file for aligners and most analysis tasks, a version called "analysisSet" for the human genome. </li> <li> The <b>p14/</b> subdirectory contains files for GRCh38.p14 (patch release 14), which has 711 sequences, 351 alternate sequences, and 166 fix sequences. </li> <li> @@ -3877,33 +3877,33 @@ fix patch sequences (not all of which are included in UCSC's hg19).</p> <p> dbSNP build 155 is composed of 5 subtracks: <ul> <li><b>Common dbSNP(155)</b> - Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants</li> <li><b> ClinVar dbSNP(155)</b> - Short Genetic Variants in ClinVar</li> <li><b>Mult. dbSNP(155)</b> - Short Genetic Variants that map to multiple genomic loci</li> <li><b>All dbSNP(155)</b> - All Short Genetic Variants</li> <li><b>Map Err dbSnp(155)</b> - Mappings with Inconsistent Coordinates</li> </ul></p> <h3>Data Access</h3> <p> The complete data can be found across two separate directories in our download server, a bigBed file -(bigDbSnp) for <a target="_blank" href="http://hgdownload.soe.ucsc.edu/gbdb/hg19/snp/">hg19</a> -and <a target="_blank" href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/">hg38</a>, and a -<a target="_blank" href="http://hgdownload.soe.ucsc.edu/gbdb/hgFixed/dbSnp/">shared secondary +(bigDbSnp) for <a target="_blank" href="http://hgdownload.gi.ucsc.edu/gbdb/hg19/snp/">hg19</a> +and <a target="_blank" href="http://hgdownload.gi.ucsc.edu/gbdb/hg38/snp/">hg38</a>, and a +<a target="_blank" href="http://hgdownload.gi.ucsc.edu/gbdb/hgFixed/dbSnp/">shared secondary details file</a> which holds additional variant details.<p> </p> <p> We would like to thank the dbSNP group at NCBI for providing access to these data. We would also like to thank Galt Barber, Angie Hinrichs, and Gerardo Perez for their efforts on this release. </p> <a name="080222"></a> <h2>Aug. 08, 2022 New GENCODE gene tracks: Human V41 (hg19/hg38) - Mouse VM30 (mm39)</h2> <p> We are pleased to announce new GENCODE Gene annotation tracks, which correspond to <a href="https://www.ensembl.info/2022/05/31/whats-coming-in-ensembl-release-107-ensembl-genomes-54/" @@ -4058,31 +4058,31 @@ <a name="052422"></a> <h2>May 24, 2022 New Assembly Request Page</h2> <p> Find the genome of your favorite organism on our new <a href="/assemblyRequest.html" target="_blank">assembly request</a> page. Click "view" to launch a browser, or the "request" button to request that we add yours.</p> <div class="text-center"> <a href="/assemblyRequest.html"> <img src="../images/newsArchImages/requestPage.png" alt="New Assembly Request Page" width="700"> </a> </div> <p>Our most recent blog post, -<a href="https://genome-blog.soe.ucsc.edu/blog/2022/04/12/genark-hubs-part-4/" +<a href="https://genome-blog.gi.ucsc.edu/blog/2022/04/12/genark-hubs-part-4/" target="_blank">GenArk Hubs Part 4 - New assembly request page</a> describes how to use this new feature.</p> <p> With the realization that we could not possibly host every single genomic assembly available, we created <a href="help/hgTrackHubHelp.html#Assembly" target="_blank">Assembly Hubs</a>. Assembly Hubs allow anyone to host and view the genome of any species in the context of the UCSC Genome Browser. Last summer we <a href="newsarch.html#060121">announced</a> the creation of the Genome Archive (GenArk) which included Assembly Hubs for the genomic assemblies of more than 1,300 species. Since then, we have taken this a step further by creating this new <a href="/assemblyRequest.html" target="_blank">Assembly Request</a> page that displays about 14,000 assemblies: those that are available for viewing and those that can be requested. We currently have nearly 1,700 assembly hubs available for viewing at the click of a button. Upon first visiting the page shows only <b>the first 500 assemblies</b>. Use the <em>select assembly type to display</em> button to "show all" assemblies. If you don't see the organism or assembly you are interested in then please use the page to request it. We will build an Assembly Hub for you @@ -4386,31 +4386,31 @@ </p> <a name="041222"></a> <h2>Apr. 12, 2022 T2T CHM13 v2.0 now available in the Genome Browser</h2> <p> The Genome Browser has a <a href="/goldenPath/history.html">rich history</a> intricately connected to human genomic research. We have provided display to almost two dozen human genomes beginning with the first drafts in the year 2000. Nearly 22 years later, the <a href="https://sites.google.com/ucsc.edu/t2tworkinggroup" target="_blank">T2T consortium</a> has published the most complete human haploid genome sequence to date, having added just about all of the 200 million bases (8%) missing from the current reference. We are proud of all the scientists involved, including our colleagues in the <a href="https://genomics.ucsc.edu/" target="_blank">UCSC Genomics Institute</a>, who played a role in this release. We strive to facilitate omics research and thus would like to announce our expanded support for the <a -href="/cgi-bin/hgTracks?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt&genome=GCA_009914755.4&position=lastDbPos" +href="/cgi-bin/hgTracks?hubUrl=https://hgdownload.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt&genome=GCA_009914755.4&position=lastDbPos" target="_blank">T2T-CHM13 v2.0 browser</a>.</p> <a name="CHM13"></a><h3>What is T2T-CHM13 v2.0?</h3> <p> <a href="https://www.science.org/doi/10.1126/science.abj6987" target="_blank">T2T-CHM13 v2.0</a> was produced by sequencing the CHM13hTERT human cell line from a hydatiform mole, which is haploid, meaning it contains nearly uniform homozygosity. It also employed recent technologies such as <a target="_blank" href="https://www.pacb.com/technology/hifi-sequencing/">HiFi</a> and <a target="_blank" href="https://nanoporetech.com/">nanopore</a> sequencing. The result is a 3.055 billion base pair genome that includes gapless assemblies for all main chromosomes and introduces nearly 200 Mbp of novel sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes. A Y chromosome was added from Genome in a Bottle's HG002 sample.</p> @@ -4502,60 +4502,60 @@ <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hub_3267197_GCA_009914755.4&c=CP068277.2&g=hub_3267197_hgLiftOver" target="_blank">Human liftOver</a> - Contains one to one Nextflow LiftOver pipeline alignments between CHM13 and hg19/hg38.</li> <li><a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hub_3267197_GCA_009914755.4&c=CP068277.2&g=hub_3267197_GCA_009914755_4_T2T-CHM13v2_0ChainNet" target="_blank">Chain/Net Track</a> - Alignment track between CHM13 and four other human genomes that shows rearrangements in our usual chains (=alignable) and net (=synteny) display formats. Other genomes are hg19, hg38, HG002pat, and HG002mat.</li></ul></p> <h3>How to display my data in CHM13?</h3> <p> We have added support for CHM13 to our <a href="/cgi-bin/hgConvert?db=hg38&position=lastDbPos" target="_blank">hgConvert tool</a>. This allows region conversion of the current viewing window between hg19/hg38 to CHM13 and vice versa. We will also be adding support for conversion of data using our <a href="/cgi-bin/hgLiftOver" target="_blank">hgLiftOver tool</a> at our next version release on May 3rd. In the meantime, the command line version of -<a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" +<a href="https://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads" target="_blank">liftOver</a> in combination with the proper <a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/liftOver/">chain file</a> can be used to lift annotations.</p> <figure class="text-center"> <img class='text-center' src="../images/hgConvert.png" width='80%' alt="Using hgConvert tool to see coordinates between hg38 and CHM13."> </figure> <p> <a href="/cgi-bin/hgCustom" target="_blank">Custom tracks</a> and <a href="/cgi-bin/hgHubConnect" target="_blank">track hubs</a> can also be used to display annotations on CHM13. In the case of track hubs, using <code>genome GCA_009914755.4</code> is sufficient to declare the assembly. We have also expanded our support of variable chromosome names, so data can be loaded using either UCSC ("chr1"), NCBI ("CP068277.2") or Ensembl ("1") sequence identifiers. <b>There should no longer be a need to convert sequence names</b>.</p> <p> It is worth noting that GenArk assemblies are functionally hubs, which means all data is stored in binary files, not MySQL databases. If your existing data pipelines do not work because our data formats have changed compared to hg19/hg38, please do not hesitate to contact us. Most formats are very similar to the MySQL tables and we have command line tools that can perform the conversions.</p> <h3>Where to download CHM13 data?</h3> <p> All GenArk hubs are hosted on our download server. This means that all settings information and data for displaying this browser can be found there: -<a href="https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/" -target="_blank">https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/</a></p> +<a href="https://hgdownload.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/" +target="_blank">https://hgdownload.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/</a></p> <p> We also provide FASTA files there with two different sequence identifiers (the "chr1" format and Genbank accessions), gene annotations in GFF and other formats and assembly indexes with either Genbank or "chr1" sequence names for the aligners bwa-mem2, bowtie2, hisat2 and minimap2. Detailed download instructions can be found in the README and on our <a href="https://genome.ucsc.edu/cgi-bin/hgGateway?db=hub_3267197_GCA_009914755.4" target="_blank">assembly description page</a></p> <p> All liftOver files, including files to/from hg19/hg38 and CHM13 can also be found on our download server: <a href="https://hgdownload.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/liftOver/" target="_blank">https://hgdownload.gi.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/liftOver/</a></p> <h3>Acknowledgments</h3> @@ -4835,31 +4835,31 @@ <p> The JASPAR database is a joint effort between several labs (please see the latest <a href="https://www.ncbi.nlm.nih.gov/pubmed/34850907" target="_blank">JASPAR paper</a>). Binding site predictions and UCSC tracks were computed by the <a href="http://cisreg.ca/" target="_blank">Wasserman Lab</a>. We would like to thank Daniel Schmelter and Jairo Navarro at UCSC for building and testing these tracks.</p> <!-- ============= 2021 archived news ============= --> <a name="2021"></a> <a name="122021"></a> <h2>Dec. 20, 2021 Last of three blog posts about new GenArk hubs</h2> <p> We are pleased to announce the third blog post in a three-part series about our new GenArk Assembly Hubs. -This <a href="https://genome-blog.soe.ucsc.edu/blog/2021/12/20/genark-hubs-part-3/" +This <a href="https://genome-blog.gi.ucsc.edu/blog/2021/12/20/genark-hubs-part-3/" target="_blank">final installment</a> provides some explanation of the technical details behind the process. The <a href="https://bit.ly/UCSC_blog_GenArk1">first post</a> was about accessing the data, and the <a href="https://bit.ly/UCSC_blog_GenArk2">second post</a> shared examples of using the hub's data with BLAT, PCR, and External Tools.</p> <a name="121621"></a> <h2>Dec. 16, 2021 Track Hub Filters Quick Start Guide</h2> <p> We are pleased to announce a help page specific to building filters on Track Hubs. <a href="help/hgTrackHubHelp.html#Intro">Track Hubs</a> are web-accessible directories of genomic data that can be viewed on the UCSC Genome Browser. Track Hubs allow a lab to share and host all their genomic data (<a href="help/bam.html">BAMs</a>, <a href="help/vcf.html">VCFs</a>, ect.) via a single Genome Browser link. Such links can load multiple hubs and even be combined with a position parameter to easily reference laboratory data around a gene of interest, see examples in a recent <a href="https://bit.ly/UCSC_blog_sharing">blog bost</a> about sharing data with URLs.</p> @@ -4897,31 +4897,31 @@ </p> <p> Each section of the <a href="help/hubQuickStartFilter.html">Track Hub Filters Quick Start Guide</a> comes with examples and sessions allowing to quickly click into real interactive demonstration hubs to experiment with how the settings work. The example hubs also provide a starter template for building similar hubs.</p> <p> Many thanks to Lou Nassar for building this Filters Quick Start Guide and Brian Raney for his work implementing the new filter software.</p> <a name="120621"></a> <h2>Dec. 6, 2021 Second of three blog posts about new GenArk hubs</h2> <p> We are pleased to announce the second blog post in a three-part series about our new GenArk Assembly Hubs. -This <a href="https://genome-blog.soe.ucsc.edu/blog/2021/12/06/genark-hubs-part-2/" +This <a href="https://genome-blog.gi.ucsc.edu/blog/2021/12/06/genark-hubs-part-2/" target="_blank">second installment</a> provides examples of using the GenArk hubs' data with BLAT, PCR, and External Tools.</p> <a name="120321"></a> <h2>Dec. 3, 2021 Updated Variants of Concern SARS-CoV-2 track with Omicron</h2> <p> The Genome Browser has updated our <a href="/cgi-bin/hgTrackUi?db=wuhCor1&g=variantMuts"> Variants of Concern</a> track to include the latest WHO-designated variant of concern (VOC), Omicron B.1.1.529. This evolving virus has been a challenge for everyone and we are humbled to continue providing public data and our high-quality genetics research tools, now updated with the latest COVID variant information.</p> <p> This update comes as two separate subtracks to the Variants of Concern (VOC) track, one with amino acid mutations sourced from <a href="https://cov-lineages.org/" target="_blank">cov-lineages.org</a> @@ -4959,41 +4959,41 @@ <li><b>NCBI Assembly ID:</b> <a href="https://www.ncbi.nlm.nih.gov/assembly/8227741" target="_blank">8227741</a></li> <li><b>NCBI BioProject ID:</b> <a href="https://www.ncbi.nlm.nih.gov/bioproject/13179" target="_blank">13179</A></li> <li><b>NCBI BioSample ID:</b> <a href="https://www.ncbi.nlm.nih.gov/biosample/SAMN02953603" target="_blank">SAMN02953603</a></li> <li><b>Scaffold count: </b>147</li> <li><b>Total size: </b>2,312,802,198</li> <li><a href="../goldenPath/credits.html#dog_credits" target="_blank">Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#dog_use" target="_blank">Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank">Rsync</a> and - <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/canFam6/" target="_blank">FTP</a></li> - <li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#dog" target="_blank">Downloads page</a></li> + <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/canFam6/" target="_blank">FTP</a></li> + <li><a href="http://hgdownload.gi.ucsc.edu/downloads.html#dog" target="_blank">Downloads page</a></li> </ul> </p> <a name="112321"></a> <h2>Nov. 23, 2021 First of three blog posts about new GenArk hubs</h2> <p> We are pleased to announce the first blog post in a three-part series about our new GenArk Assembly Hubs. -This <a href="https://genome-blog.soe.ucsc.edu/blog/2021/11/23/genark-hubs-part-1/" +This <a href="https://genome-blog.gi.ucsc.edu/blog/2021/11/23/genark-hubs-part-1/" target="_blank">first installment</a> explains what the GenArk hubs are, and shares a number of different ways to access their over 1500 genomes.</p> <a name="111821"></a> <h2>Nov. 18, 2021 New Clinical Rare Disease track - Orphadata</h2> <p> We are happy to share another clinical resource for genetic disease correlation, <a href="/cgi-bin/hgTrackUi?db=hg38&g=orphadata">the Orphadata track</a> from <a target="_blank" href="https://www.orpha.net/">the Orphanet consortium</a>. This track shows nearly 8000 genes, on hg19 and hg38, annotated with human disorders and epidemiological information including Human Phenotype Ontology (HPO) disorder name, association type, modes of inheritance, age of first symptoms, and disease prevalence (if available). This data is gathered by a consortium of more than 40 countries, focusing on rare diseases. This track includes gene-disease display filters @@ -5335,35 +5335,35 @@ <a name="101221"></a> <h2>Oct. 18, 2021 Addition of GRCh38 patch 13 sequences to hg38</h2> <p> We are pleased to announce the addition of GRCh38 patch release 13 to the <a href="../../cgi-bin/hgGateway?db=hg38">hg38</a> assembly. hg38 has been updated with patches since its release in 2013. The GRC patch releases do not change any previously existing sequences; they simply add new sequences for fix patches or alternate haplotypes that correspond to specific regions of the main chromosome sequences. For most users, the patches are unlikely to make a difference and may complicate the analysis as they introduce more duplication.</p> <p> More information on how patch sequences are incorporated can be found on the <a href="https://genome-blog.gi.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. The blog post contains details about the new -<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/latest/" +<a href="https://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/latest/" target="_blank">/latest</a>, -<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/initial/" +<a href="https://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/initial/" target="_blank">/initial</a>, and -<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/p13/" target="_blank">/p13</a> +<a href="https://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/p13/" target="_blank">/p13</a> download directories on the downloads server. With the addition of new sequences to hg38, we can expect to see BLAT return more matches to the genome.</p> <ul> <li> The <b>initial/</b> subdirectory contains files for the initial release of GRCh38, which has 455 sequences, 261 alternate sequences, and no fix sequences. It is the same as the parent download directory. This is probably the best genome file for aligners and most analysis tasks, a version called "analysisSet" for the human genome. </li> <li> The <b>p13/</b> subdirectory contains files for GRCh38.p13 (patch release 13). It has 640 sequences including alternate and fix sequences. </li> <li> @@ -5453,35 +5453,35 @@ <a name="080421"></a> <h2>Aug. 04, 2021 Addition of GRCm38 patch 6 sequences to mm10</h2> <p> We are pleased to announce the addition of GRCm38 patch release 6 to the mm10 assembly. mm10 has been updated with patches since its release in 2012. The GRC patch releases do not change any previously existing sequences; they simply add new sequences for fix patches or alternate haplotypes that correspond to specific regions of the main chromosome sequences. For most users, the patches are unlikely to make a difference and may complicate the analysis as they introduce more duplication.</p> <p> More information on how patch sequences are incorporated can be found on the <a href="https://genome-blog.gi.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. The blog post contains details about the new -<a href="https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/latest/" +<a href="https://hgdownload.gi.ucsc.edu/goldenPath/mm10/bigZips/latest/" target="_blank">/latest</a>, -<a href="https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/initial/" +<a href="https://hgdownload.gi.ucsc.edu/goldenPath/mm10/bigZips/initial/" target="_blank">/initial</a>, and -<a href="https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/p6/" target="_blank">/p6</a> +<a href="https://hgdownload.gi.ucsc.edu/goldenPath/mm10/bigZips/p6/" target="_blank">/p6</a> download directories on the downloads server. With the addition of new sequences to mm10, we can expect to see BLAT return more matches to the genome.</p> <ul> <li> The <b>initial/</b> subdirectory contains files for the initial release of GRCm38, which has 66 sequences, no original alternate sequences, and no fix sequences. It is the same as the parent download directory. This is probably the best genome file for aligners and most analysis tasks, a version called "analysisSet" for the human genome. </li> <li> The <b>p6/</b> subdirectory contains files for GRCm38.p6 (patch release 6). It has 239 sequences including alternate and fix sequences. Note that these patches include "strain-specific" sequences. You may want to check with the authors of your aligner if the software can recognize these sequences. @@ -5516,33 +5516,33 @@ <li><B>NCBI BioProject ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/bioproject/577946' TARGET='_blank'>577946</A></li> <li><B>NCBI BioSample ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/biosample/SAMN13041969' TARGET='_blank'>SAMN16261960</A></li> <li><b>Scaffold count: </b>167</li> <li><b>Total size: </b>1,451,301,209</li> <li><a href="../goldenPath/credits.html#xentro_credits" target="_blank" >Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#xentro_use" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a> and -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/xenTro10/" +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/xenTro10/" target="_blank" >FTP</a></li> - <li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#xentro" + <li><a href="http://hgdownload.gi.ucsc.edu/downloads.html#xentro" target="_blank" >Downloads page</a></li> </ul> </p> <p> We would like to thank the University of California, Berkeley for creating this new X. tropicalis assembly. We would also like to thank Hiram Clawson, Lou Nassar, and Gerardo Perez for the development and release of the xenTro10 genome browser. </p> <a name="072021"></a> <h2>July 20, 2021 Updated GENCODE tracks released for hg38, hg19, and mm39</h2> <p> We have updated our GENCODE gene datasets to the latest releases; v38 for human (hg38 & hg19) and v27 for the mouse genome assembly (mm39). These new annotation data were released by GENCODE in May 2021 @@ -5822,100 +5822,100 @@ <li><b>RefSeq Diffs</b> – alignment differences between the human reference genome(s) and RefSeq transcripts <li><b>RefSeq Select</b> – a single Select transcript representative for each protein-coding gene <li><b>RefSeq HGMD</b> – transcripts with clinical variants in Human Gene Mutation Database </ul> <p> We would like to thank NCBI and the RefSeq Annotation database for collecting and curating these data. We would also like to thank Hiram Clawson, Lou Nassar, and Gerardo Perez for developing and releasing these tracks. </p> <a name="060121"></a> <h2>June 1, 2021 Genome Archive (GenArk) hubs and Dynamic BLAT</h2> <p> Do you have a favorite species or a research organism for which you'd like to visualize the genomic sequence? With the recent addition of genomic assemblies for more than 1,300 species, it's possible that your favorite is now available in the UCSC Genome Browser. -Check <a href="https://hgdownload.soe.ucsc.edu/hubs/">this list</a> of new assemblies +Check <a href="https://hgdownload.gi.ucsc.edu/hubs/">this list</a> of new assemblies to see if yours is a click away. Each of these Genome Browser assembly hubs comes pre-loaded with several annotation tracks, gene models, and the ability to align genomic sequence to the reference assembly using the <a href="/FAQ/FAQblat.html">BLAT</a> alignment tool. You can add your own data to your view of the assembly hub by uploading a <a href="help/customTrack.html">custom track</a> or creating a <a href="help/hgTrackHubHelp.html">track hub</a>.</p> <p> -We call this group of assembly hubs, the <a href=https://hgdownload.soe.ucsc.edu/hubs/> +We call this group of assembly hubs, the <a href=https://hgdownload.gi.ucsc.edu/hubs/> Genome Archive (GenArk)</a>. The genomes in the GenArk are sourced from <a href=https://www.ncbi.nlm.nih.gov/refseq/ target="_blank">NCBI RefSeq</a>, the <a href="https://vertebrategenomesproject.org/" target="_blank">Vertebrate Genomes Project (VGP)</a> and other projects. See the complete list of assembly hubs <a target="_blank" -href="https://hgdownload.soe.ucsc.edu/hubs/UCSC_GI.assemblyHubList.txt">here</a>.</p> +href="https://hgdownload.gi.ucsc.edu/hubs/UCSC_GI.assemblyHubList.txt">here</a>.</p> <p> GenArk assemblies can be found by searching the common name (e.g. <a href="../h/GCF_001984765.1">American Beaver</a>) or GCA/GCF accession (e.g. <a href="../h/GCF_001984765.1">GCF_001984765.1</a>) directly on the <a href="/cgi-bin/hgGateway">Genome Browser Gateway page</a>. A full list can also be seen on the <a -href="https://hgdownload.soe.ucsc.edu/hubs">GenArk portal</a> which +href="https://hgdownload.gi.ucsc.edu/hubs">GenArk portal</a> which is organized by phylogenetic groups and projects:<br> <div align="left"> <table class="stdTbl"> - <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/primates/index.html">Primates</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/primates/asmStats.html">Assembly statistics</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/primates/trackData.html">Track statistics</a></td></tr> + <tr><td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/primates/index.html">Primates</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/primates/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/primates/trackData.html">Track statistics</a></td></tr> - <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/mammals/index.html">Mammals</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/mammals/asmStats.html">Assembly statistics</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/mammals/trackData.html">Track statistics</a></td></tr> + <tr><td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/mammals/index.html">Mammals</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/mammals/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/mammals/trackData.html">Track statistics</a></td></tr> - <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/birds/index.html">Birds</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/birds/asmStats.html">Assembly statistics</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/birds/trackData.html">Track statistics</a></td></tr> + <tr><td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/birds/index.html">Birds</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/birds/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/birds/trackData.html">Track statistics</a></td></tr> - <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/fish/index.html">Fishes</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/fish/asmStats.html">Assembly statistics</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/fish/trackData.html">Track statistics</a></td></tr> + <tr><td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/fish/index.html">Fishes</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/fish/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/fish/trackData.html">Track statistics</a></td></tr> - <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/vertebrate/index.html">Vertebrates</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/vertebrate/asmStats.html">Assembly statistics</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/vertebrate/trackData.html">Track statistics</a></td></tr> + <tr><td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/vertebrate/index.html">Vertebrates</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/vertebrate/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/vertebrate/trackData.html">Track statistics</a></td></tr> - <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/invertebrate/index.html">Invertebrates</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/invertebrate/asmStats.html">Assembly statistics</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/invertebrate/trackData.html">Track statistics</a></td></tr> + <tr><td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/invertebrate/index.html">Invertebrates</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/invertebrate/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/invertebrate/trackData.html">Track statistics</a></td></tr> - <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/fungi/index.html">Fungi</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/fungi/asmStats.html">Assembly statistics</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/fungi/trackData.html">Track statistics</a></td></tr> + <tr><td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/fungi/index.html">Fungi</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/fungi/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/fungi/trackData.html">Track statistics</a></td></tr> - <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/plants/index.html">Plants</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/plants/asmStats.html">Assembly statistics</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/plants/trackData.html">Track statistics</a></td></tr> + <tr><td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/plants/index.html">Plants</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/plants/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/plants/trackData.html">Track statistics</a></td></tr> - <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/VGP/index.html">VGP</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/VGP/asmStats.html">Assembly statistics</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/VGP/trackData.html">Track statistics</a></td></tr> + <tr><td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/VGP/index.html">VGP</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/VGP/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/VGP/trackData.html">Track statistics</a></td></tr> - <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/legacy/index.html">Legacy</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/legacy/asmStats.html">Assembly statistics</a></td> - <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/legacy/trackData.html">Track statistics</a></td></tr> + <tr><td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/legacy/index.html">Legacy</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/legacy/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/legacy/trackData.html">Track statistics</a></td></tr> - <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/globalReference/index.html">Global Reference</a></td> + <tr><td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/globalReference/index.html">Global Reference</a></td> <td><a></a></td> <td><a></a></td></tr> - <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hubIndex.html">Mouse Strains</a></td> + <tr><td><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/mouseStrains/hubIndex.html">Mouse Strains</a></td> <td><a></a></td> <td><a></a></td></tr> </table></div></p> <p> The number of NCBI RefSeq assemblies has been increasing each year, and we expect the trend to continue as assemblies from VGP, and other projects are released. Our next step is to add additional clades to GenArk including archaea, viruses, and bacteria.</p> <p> As mentioned above, assembly hubs in the GenArk allow for sequence alignment using the BLAT tool. We extended our traditional <a href="../cgi-bin/hgBlat?command=start">BLAT tool</a> to accommodate these assembly hubs and we call it Dynamic BLAT. Dynamic BLAT pre-computes index genomes files, which allows assemblies to have a BLAT server without needing it to be resident in the computer's memory. Dynamic BLAT allows us to offer BLAT services on nearly all of our GenArk assemblies, with a few exceptions due to excessive genome size.</p> @@ -5981,33 +5981,33 @@ <li><B>NCBI BioProject ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/bioproject/662791' TARGET='_blank'>662791</A></li> <li><B>NCBI BioSample ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/biosample/SAMN16261960' TARGET='_blank'>SAMN16261960</A></li> <li><b>Scaffold count: </b>176</li> <li><b>Total size: </b>2,647,915,728</li> <li><a href="../goldenPath/credits.html#rat_credits" target="_blank" >Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#rat_use" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a> and -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/rn7/" +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/rn7/" target="_blank" >FTP</a></li> - <li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#rat" + <li><a href="http://hgdownload.gi.ucsc.edu/downloads.html#rat" target="_blank" >Downloads page</a></li> </ul> </p> <p> We would like to thank the Darwin Tree of Life Project at the Wellcome Sanger Institute for creating this new rat assembly. We would also like to thank Hiram Clawson, Lou Nassar, and Gerardo Perez for the development and release of the rn7 genome browser. </p> <a name="041321"></a> <h2>Apr. 13, 2021 New Haploinsufficiency predictions for human (hg19)</h2> <p> We are happy to announce a new haploinsufficiency predictions track for human assembly <a href="/cgi-bin/hgTrackUi?db=hg19&c=chrX&g=decipherHaploIns">GRCh37/hg19</a>. This track displays haploinsufficiency predictions for human genes from @@ -6370,34 +6370,34 @@ <li><b>Scaffold count:</b> 994</li> <li><b>Total size:</b> 2,897,824,427</li> <li> <a href="../goldenPath/credits.html#marmoset_credits" target="_blank">Acknowledgments</a> </li> </ul> <h3>Data and Downloads:</h3> <ul> <li> <a href="../goldenPath/credits.html#marmoset_use" target="_blank">Data use conditions and restrictions</a> </li> <li> <a href="../goldenPath/help/ftp.html" target="_blank">Rsync</a> and - <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/calJac4/" target="_blank">FTP</a> + <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/calJac4/" target="_blank">FTP</a> </li> <li> - <a href="http://hgdownload.soe.ucsc.edu/downloads.html#marmoset" target="_blank">Downloads + <a href="http://hgdownload.gi.ucsc.edu/downloads.html#marmoset" target="_blank">Downloads page</a> </li> </ul> <a name="020321"></a> <h2>Feb. 3, 2021 New Exome Sequencing Probesets for human (hg38/hg19)</h2> <p> In our effort to better support personalized medicine and clinical genetics researchers, we are happy to announce the addition of 78 new whole exome sequencing (WES) probes and targets tracks from several major companies for human genomes hg38 and hg19. Our new tracks include data on WES kits from Illumina, Agilent, Roche, IDT, Twist, and MGI (BGI). Understanding exome sequencing probes and targets helps bring awareness to the different gene isoforms and alternative splicing that may be important for disease research. You can find these tracks under the "Mapping and Sequencing" group or go directly to the description pages of the "Exome Probesets" tracks below:</p> @@ -6486,33 +6486,33 @@ <li><B>NCBI BioProject ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/bioproject/318403' TARGET='_blank'>318403</A></li> <li><B>NCBI BioSample ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/biosample/SAMN04851098' TARGET='_blank'>SAMN04851098</A></li> <li><b>Scaffold count: </b>794</li> <li><b>Total size: </b>2,343,218,756</li> <li><a href="../goldenPath/credits.html#dog_credits" target="_blank" >Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#dog_use" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a> and -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/canFam5/" +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/canFam5/" target="_blank" >FTP</a></li> - <li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#dog" + <li><a href="http://hgdownload.gi.ucsc.edu/downloads.html#dog" target="_blank" >Downloads page</a></li> </ul> </p> <a name="012221"></a> <h2>Jan. 22, 2021 Updates to gnomAD variation track (GRCh37/hg19)(GRCh38/hg38)</h2> <p> We are pleased to announce updates to the gnomAD Variants super-track for the <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg19&c=chrX&g=gnomadSuper">hg19/GRCh37</a> and <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=gnomadVariants">hg38/GRCh38</a> human assemblies.</p> <ul> <li>gnomAD v3.1 is now available and contains variants from 76,156 whole genomes (and no exomes), all mapped to the GRCh38/hg38 reference sequence. 4,454 genomes were added to the number of @@ -6625,54 +6625,54 @@ hg19</a>) - This track set shows the results of the <a target="_blank" href="https://www.covid19hg.org/blog/2020-11-24-covid-19-hgi-results-for-data-freeze-4-october-2020/"> GWAS Data Release 4 (October 2020)</a> from the <a target="_blank" href="https://www.covid19hg.org/"> COVID-19 Host Genetics Initiative (HGI)</a> which aims to identify the genetic determinants of SARS-CoV-2 infection susceptibility, disease severity and outcomes.</li> <li> <a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=sarsCov2PhyloPub"> Updated - Phylogenetic Tree and Variants from High-coverage Sequences in Public Databases</a> - Updated from release <b>28-08-20</b> to <b>28-10-20</b>. This track displays a phylogenetic tree inferred from SARS-CoV-2 genome sequences from <a href="https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=SARS-CoV-2,%20taxid:2697049" target="_blank">GenBank</a>, <a href="https://www.cogconsortium.uk/data/" target="_blank">COG-UK</a> and the <a href="https://bigd.big.ac.cn/ncov/release_genome" target="_blank">China National Center for Bioinformation</a>, and variants found in the sequences. Since this track is sourced from public databases, we can offer VCF files with -sequence variants for <a href="https://hgdownload.soe.ucsc.edu/gbdb/wuhCor1/sarsCov2PhyloPub/" +sequence variants for <a href="https://hgdownload.gi.ucsc.edu/gbdb/wuhCor1/sarsCov2PhyloPub/" target="_blank">download</a>.</li> </ul> <p><br> We would like to thank the publication authors <a target="_blank" href="https://www.ncbi.nlm.nih.gov/pubmed/32895485">Li <em>et al</em></a> and <a target="_blank" href="https://www.biorxiv.org/content/10.1101/2020.11.06.372037v1">Liu <em>et al</em></a> for making these data available. We would also like to thank <a href="http://public.gi.ucsc.edu/~jferna10/" target="_blank">Jason Fernandes</a>, <a href="https://www.cogconsortium.uk/" target="_blank">COG-UK</a>, <a href="https://www.ncbi.nlm.nih.gov/genbank/" target="_blank">GenBank</a>, the <a href="https://gisaid.org/" target="_blank">GISAID Initiative</a>, the <a href="https://www.covid19hg.org/" target="_blank">COVID-19 Host Genetics Initiative (HGI)</a> and their <a target="_blank" href="https://www.covid19hg.org/partners/">partners</a>, as well as Rachel Liao, Juha Karjalainen, and Kumar Veerapen from the <a target="_blank" href="https://www.broadinstitute.org/">Broad Institute</a>.</p> <p> These tracks are made possible due to the worldwide efforts of scientists, including the <a href="/staff.html" target="_blank">Genome Browser team</a>. We will continue to provide SARS-COVID-2 resources as they become available. For the latest data, see our -<a href="http://genome-preview.soe.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=lastDbPos" +<a href="http://genome-preview.gi.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=lastDbPos" target="_blank">preview site</a>. Note that content on our preview server has not undergone our QA process, and is subject to change at any time.</p> <!-- ============= 2020 archived news ============= --> <a name="2020"></a> <a name="122320"></a> <h2>Dec. 23, 2020 New ClinVar Interpretations track for human (hg19/hg38)</h2> <p> We are pleased to release a new track, <b>ClinVar Interpretations</b>, for the hg19/GRCh37 and hg38/GRCh38 human assemblies. This track can be found as part of the <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chr10&g=clinvar">ClinVar Composite</a>. It is the first track to use our bead graph display, which is a variation of our existing <a target="_blank" href="#062019">lollipop display</a>.</p> <p> @@ -6771,33 +6771,33 @@ <li><B>NCBI BioProject ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/bioproject/384558" TARGET="_blank">384558</A></li> <li><B>NCBI BioSample ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/biosample/SAMN06841387" TARGET="_blank">SAMN06841387</A></li> <li><b>Scaffold count: </b>7,873</li> <li><b>Total size: </b>2,400,934,290</li> <li><a href="../goldenPath/credits.html#hawaiian_monk_seal_credits" target="_blank" >Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#hawaiian_monk_seal_use" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a> and -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/neoSch1/" +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/neoSch1/" target="_blank" >FTP</a></li> - <li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#hawaiian_monk_seal" + <li><a href="http://hgdownload.gi.ucsc.edu/downloads.html#hawaiian_monk_seal" target="_blank" >Downloads page</a></li> </ul> </p> <p> We would like to thank Alan F. Scott at Johns Hopkins University and NCBI for creating this new Hawaiian monk seal assembly. We would also like to thank Hiram Clawson, Robert Kuhn, and Gerardo Perez for the development and release of the neoSch1 genome browser. </p> <a name="120220"></a> <h2>Dec. 2, 2020 New and updated UniProt tracks for 117 assemblies</h2> <p> We are pleased to announce new and updated <a href="https://www.uniprot.org/" target="_blank"</a>UniProt tracks</a> for the following assemblies:</p><br> @@ -7141,32 +7141,32 @@ NCBI Genome ID: <a href="https://www.ncbi.nlm.nih.gov/genome/52" target="_blank">52</a> (Mus musculus)</li> <li> NCBI Assembly ID: <a href="https://www.ncbi.nlm.nih.gov/assembly/7358741" target="_blank">7358741</a></li> <li> NCBI BioProject ID: <a href="https://www.ncbi.nlm.nih.gov/bioproject/20689" target="_blank">20689</a></li> </ul> <p> For more information about the files included in the GRCm39 GenBank submission, see the <a href="https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.9_GRCm39/README.txt" target="_blank">GRCm39 README</a>. The GRCm39 GenBank record provides a detailed array of <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.27/" target="_blank">statistics about this assembly</a>. Bulk downloads of the sequence and annotation data may be obtained from the -Genome Browser <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/mm39/">FTP server</a> or -the <a href="http://hgdownload.soe.ucsc.edu/downloads.html#mouse" target="_blank">Downloads +Genome Browser <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/mm39/">FTP server</a> or +the <a href="http://hgdownload.gi.ucsc.edu/downloads.html#mouse" target="_blank">Downloads page</a>. The annotation tracks for this browser were generated by UCSC and collaborators worldwide.</p> <p> We would like to thank the GRC and NCBI for creating this new mouse assembly. We would also like to thank Hiram Clawson and Jairo Navarro for the development and release of the mm39 genome browser. </p> <a name="102120"></a> <h2>Oct. 21, 2020 October 21st release for SARS-CoV-2 genome browser</h2> <p> We are pleased to announce our fourth data release for the <a href="/cgi-bin/hgTracks?db=wuhCor1" target="_blank">coronavirus genome browser</a>. (See also our <a href="#040320">first</a>, <a href="#050420">second</a>, and <a href="#080720">third</a> releases)</p> <p> @@ -7233,31 +7233,31 @@ identify selection sites of interest in SARS-CoV-2 data from <a href="https://www.gisaid.org/about-us/mission/" target="_blank">GISAID</a>.</li> <li> <a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=sarsCov2PhyloPub"> Phylogenetic Tree and Variants from High-coverage Sequences in Public Databases</a> - This track displays a phylogenetic tree inferred from SARS-CoV-2 genome sequences from <a href="https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=SARS-CoV-2,%20taxid:2697049" target="_blank">GenBank</a>, <a href="https://www.cogconsortium.uk/data/" target="_blank">COG-UK</a> and the <a href="https://bigd.big.ac.cn/ncov/release_genome" target="_blank">China National Center for Bioinformation</a>, and variants found in the sequences. It uses the phylogenetic tree from the <a href="https://github.com/roblanf/sarscov2phylo/releases/tag/28-08-20" target="_blank">sarscov2phylo 28-08-20</a> release, pruned to include only public sequences. Since the public sequences are unrestricted, we can offer VCF files with -sequence variants for <a href="https://hgdownload.soe.ucsc.edu/gbdb/wuhCor1/sarsCov2PhyloPub/" +sequence variants for <a href="https://hgdownload.gi.ucsc.edu/gbdb/wuhCor1/sarsCov2PhyloPub/" target="_blank">download</a>.</li> <li> <a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=Starr_Bloom_antibody"> Spike protein receptor-binding domain (S RBD) Deep Mutational Scanning</a> - Tracks created from this data include:<ul> <li> <a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=Starr_Bloom_antibody"> S RBD Deep Mutational Scanning: Antibody Escape</a> - This track shows deep mutational scanning data measuring the effect of the mutations to the Spike RBD to binding of antibodies using a yeast surface display system.</li> <li> <a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=Starr_Bloom_bind"> S RBD Deep Mutational Scanning: ACE2 Binding</a> - This track shows deep mutational scanning data measuring effect of all possible point (amino acid) RBD mutations on ACE2 binding affinity using a yeast surface display system.</li> @@ -7293,31 +7293,31 @@ We would also like to thank <a href="http://www.robertlanfear.com/" target="_blank"> Rob Lanfear</a>, <a href="https://www.biorxiv.org/content/10.1101/2020.06.02.130955v1" target="_blank">Irwin Jungreis</a>, <a href="http://zhanglab.net/" target="_blank"> Qiangfeng Cliff Zhang</a>, <a href="http://public.gi.ucsc.edu/~jferna10/" target="_blank"> Jason Fernandes</a>, <a href="https://snerli.wordpress.com/about/" target="_blank"> Santrupti Nerli</a>, <a href="https://www.lji.org/faculty-research/labs/peters/#overview" target="_blank">Bjoern Peters</a>, the <a href="https://research.fhcrc.org/bloom/en.html" target="_blank">Bloom Lab</a>, the <a href="https://www.weizmann.ac.il/pages/" target="_blank">Weizmann Institute of Science</a> and the <a href="https://gisaid.org/" target="_blank">GISAID Initiative</a>.</p> <p> These tracks are made possible due to the worldwide efforts of scientists, including the <a href="/staff.html" target="_blank">Genome Browser team</a>. We will continue to provide SARS-COVID-2 resources as they become available. For the latest data, see our -<a href="http://genome-preview.soe.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=lastDbPos" +<a href="http://genome-preview.gi.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=lastDbPos" target="_blank">development site</a>. Note that content on our preview server has not undergone our QA process, and is subject to change at any time.</p> <a name="101520"></a> <h2>Oct. 15, 2020 Updated Ensembl gene tracks for 47 assemblies (v101)</h2> <p> We are pleased to announce an update to the <a href="http://uswest.ensembl.org/info/genome/genebuild/index.html" target="_blank"> Ensembl gene annotation</a> tracks to <strong>v101</strong> for the following assemblies:</p><br> <div class="container"> <div class="row"> <div class="col-sm-4"> <ul> <li>Armadillo <a href="../cgi-bin/hgTrackUi?db=dasNov3&g=ensGene" @@ -7721,32 +7721,32 @@ TARGET='_blank'>4438481</A></li> <li><B>NCBI BioProject ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/bioproject/369439' TARGET='_blank'>369439</A></li> <li><B>NCBI BioSample ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/biosample/SAMN11078986' TARGET='_blank'>SAMN11078986</A></li> <li><b>Scaffold count: </b>5486</li> <li><b>Total size: </b>3,044,872,214</li> <li><a href="../goldenPath/credits.html#gorilla_credits">Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#gorilla_use" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a></li> - <li>FTP: <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/gorGor6/" >Gorilla</a></li> - <li>Downloads page: <a href="http://hgdownload.soe.ucsc.edu/downloads.html#gorilla">Gorilla</a> + <li>FTP: <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/gorGor6/" >Gorilla</a></li> + <li>Downloads page: <a href="http://hgdownload.gi.ucsc.edu/downloads.html#gorilla">Gorilla</a> </li> </ul> </p> <a name="082120"></a> <h2>Aug. 21, 2020 Wildfires in Santa Cruz County</h2> <p> Northern California and the county of Santa Cruz are experiencing serious wildfires, including in the Santa Cruz mountains just north of UCSC campus. Campus has been evacuated and shutdowns are occurring. We believe that the Genome Browser will not be affected, but it is possible that if power is lost, backup power will not last indefinitely. @@ -7785,31 +7785,31 @@ <p> We should add that the Browser team wishes to express our sadness and concern for the loss of property and displacement experienced by many people in the UCSC community. We are doing everything we can to help those who need it. It is possible that responses on the mailing list will be delayed. </p> <a name="080720"></a> <h2>Aug. 7, 2020 Eight new data tracks for SARS-CoV-2 (COVID) </h2> <p> We are working hard to support the scientific effort against the COVID pandemic and are happy to announce eight new annotation tracks on the SARS-CoV-2 genome. These datasets reveal information about duplication regions, sequencing, gene identities, plasmid constructs, protein contact sites, and variant distribution. Like nearly all of our tracks, the data are open-access -and downloadable through our <a href="http://hgdownload.soe.ucsc.edu/downloads.html#SARS-CoV-2"> +and downloadable through our <a href="http://hgdownload.gi.ucsc.edu/downloads.html#SARS-CoV-2"> Downloads page</a> or <a href="../../cgi-bin/hgTables">Table Browser</a> page. More information on each of these datasets can be obtained by reading the data track descriptions linked below.</p> <ul> <li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=problematicSites">Problematic sites</a> shows regions that are ambiguous and may warrant caution or masking for analysis.</li> <li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=rapid">RAPID Primers</a> marks regions that were successfully used for Nanopore sequencing. </li> <li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=unipCov2AliSwissprot">UniProt proteins</a> was updated and displays protein sequences mapped to the SARS-CoV-2 genome.</li> <li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=phyloGenes">PhyloCSF Genes</a> shows curated SARS-CoV-2 protein-coding genes conserved within the Sarbecovirus subgenus as calculated with comparative genomics algorithms.</li> <li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=addgene">AddGene Plasmid Alignments</a> describes sequences contained in Addgene plasmids that align to the SARS-CoV-2 genomes.</li> @@ -8063,49 +8063,49 @@ <li><B>NCBI BioProject ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/bioproject/526933' TARGET='_blank'>526933</A></li> <li><B>NCBI BioSample ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/biosample/SAMN11123633' TARGET='_blank'>SAMN11123633</A></li> <li><b>Scaffold count: </b>4,357</li> <li><b>Total size: </b>3,051,901,337</li> <li><a href="../goldenPath/credits.html#bonobo_credits" target="_blank" >Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#dog_use" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a></li> - <li>FTP: <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/canFam4/" + <li>FTP: <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/canFam4/" target="_blank" >Dog</a> and -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/panPan3/" +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/panPan3/" target="_blank" >Bonobo</a></li> - <li>Downloads page: <a href="http://hgdownload.soe.ucsc.edu/downloads.html#dog" + <li>Downloads page: <a href="http://hgdownload.gi.ucsc.edu/downloads.html#dog" target="_blank" >Dog</a> and -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#bonobo" +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#bonobo" target="_blank" >Bonobo</li> </ul> </p> <a name="070720"></a> <h2>Jul. 07 2020 Three new SARS-CoV-2 (COVID) variation and comparative Genomics tracks published; 20th Anniversary of the Genome Browser</h2> <h3>New SARS-CoV-2 (COVID) Tracks</h3> <p> We are pleased to announce three new SARS-CoV-2 (COVID) data track about coronavirus variation and conservation. Like nearly all of our tracks, the data are open-access -and downloadable through our <a href="http://hgdownload.soe.ucsc.edu/downloads.html#SARS-CoV-2"> +and downloadable through our <a href="http://hgdownload.gi.ucsc.edu/downloads.html#SARS-CoV-2"> Downloads page</a> or <a href="../../cgi-bin/hgTables">Table Browser</a> page. </p> <ul> <li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=PhyloCSF_smooth">PhyloCSF (Codon Substitution Frequency)</a> shows protein-coding potential score for each nucleotide in the genome in each of coding frame based on an aligning the SARS-CoV-2 genome with 44 Sarbecovirus genomes.</li> <li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=microdel">Microdeletions</a> shows sequence deletions found among thousands of SARS-CoV-2 genomes deposited in the <a href="https://www.gisaid.org/epiflu-applications/next-hcov-19-app/" target="_blank">GISAID database</a> (Global Initiative on Sharing All Influenza Data). </li> <li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=multiz7way">Human CoV</a> shows an alignment between SARS-CoV-2 and six other human-infecting coronaviruses, including SARS-CoV-1 and MERS.</li> </ul> <p> We would also like to thank the many people involved in this research and publication including the researchers Irwin Jungreis at MIT, Brianna Sierra Chrisman at Stanford, and @@ -8167,86 +8167,86 @@ <li>Part 1: Dissecting / Understanding the URL </li> <li>Part 2: Links inside genes and more tricks for links </li> <li>Part 3: Composite tracks and hosted custom tracks </li> </ul> <p> <p> Thanks to Robert Kuhn for production and to the Browser staff for all the features. <p> </p> <a name="062520"></a> <h2>Jun. 25, 2020 Vertebrate Genomes Project assembly hub update</h2> <p> -We are proud to announce our first major update to the <a href="https://hgdownload.soe.ucsc.edu/hubs/VGP/" +We are proud to announce our first major update to the <a href="https://hgdownload.gi.ucsc.edu/hubs/VGP/" target="_blank">Vertebrate Genomes Project assembly hub</a>. This is a follow up to our <a href="#082819">initial release</a>, and expands the hub to 168 assemblies.</p> <p> With this update, we have created three additional hubs in addition to the main hub:</p> <ul> -<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/VGP/index.html"> +<li><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/VGP/index.html"> <b>Primary assembly (72)</b></a> - Main hub which contains the primary assemblies for each of the organisms.</li> -<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpAlt.html"> +<li><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/VGP/vgpAlt.html"> <b>Alternate/haplotype (68)</b></a> - Secondary hub which contains alternate haplotype assemblies for a subset of the organisms in the primary hub.</li> -<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpTrio.html"> +<li><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/VGP/vgpTrio.html"> <b>Trio mat/pat (17)</b></a> - Secondary hub which contains trio assemblies (child, maternal, paternal) for a subset of the organisms in the primary hub.</li> -<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpLegacy.html"> +<li><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/VGP/vgpLegacy.html"> <b>Legacy/superseded (11)</b></a> - Hub containing previous assemblies that have since been updated.</li> </ul> <p> As with the previous release, all assemblies are built with a minimum set of data tracks including gene annotations, CpG islands, GC content, and repeat masking. <a target="_blank" -href="https://hgdownload.soe.ucsc.edu/hubs/VGP/asmStats.html">Assembly statistics</a> and -<a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/VGP/trackData.html"> +href="https://hgdownload.gi.ucsc.edu/hubs/VGP/asmStats.html">Assembly statistics</a> and +<a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/VGP/trackData.html"> track statistics</a> are also available for all hubs. Links to the different pages are included below:</p> <p> <table border='1'><thead> <tr><th colspan=5 style='text-align:center;'>Available VGP assemblies</th></tr> <tr><th>Index pages: </th> -<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/index.html'>primary assembly</a></th> -<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpAlt.html'>alternate/haplotype</a></th> -<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpTrio.html'>trio mat/pat</a></th> -<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpLegacy.html'>legacy/superseded</a></th> +<th><a href='https://hgdownload.gi.ucsc.edu/hubs/VGP/index.html'>primary assembly</a></th> +<th><a href='https://hgdownload.gi.ucsc.edu/hubs/VGP/vgpAlt.html'>alternate/haplotype</a></th> +<th><a href='https://hgdownload.gi.ucsc.edu/hubs/VGP/vgpTrio.html'>trio mat/pat</a></th> +<th><a href='https://hgdownload.gi.ucsc.edu/hubs/VGP/vgpLegacy.html'>legacy/superseded</a></th> </tr><tr> <th>Assembly statistics: </th> -<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/asmStats.html'>primary assembly</a></th> -<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpAltStats.html'>alternate/haplotype</a></th> -<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpTrioStats.html'>trio mat/pat</a></th> -<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpLegacyStats.html'>legacy/superseded</a></th> +<th><a href='https://hgdownload.gi.ucsc.edu/hubs/VGP/asmStats.html'>primary assembly</a></th> +<th><a href='https://hgdownload.gi.ucsc.edu/hubs/VGP/vgpAltStats.html'>alternate/haplotype</a></th> +<th><a href='https://hgdownload.gi.ucsc.edu/hubs/VGP/vgpTrioStats.html'>trio mat/pat</a></th> +<th><a href='https://hgdownload.gi.ucsc.edu/hubs/VGP/vgpLegacyStats.html'>legacy/superseded</a></th> </tr><tr> <th>Track statistics: </th> -<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/trackData.html'>primary assembly</a></th> -<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpAltData.html'>alternate/haplotype</a></th> -<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpTrioData.html'>trio mat/pat</a></th> -<th><a href='https://hgdownload.soe.ucsc.edu/hubs/VGP/vgpLegacyData.html'>legacy/superseded</a></th> +<th><a href='https://hgdownload.gi.ucsc.edu/hubs/VGP/trackData.html'>primary assembly</a></th> +<th><a href='https://hgdownload.gi.ucsc.edu/hubs/VGP/vgpAltData.html'>alternate/haplotype</a></th> +<th><a href='https://hgdownload.gi.ucsc.edu/hubs/VGP/vgpTrioData.html'>trio mat/pat</a></th> +<th><a href='https://hgdownload.gi.ucsc.edu/hubs/VGP/vgpLegacyData.html'>legacy/superseded</a></th> </tr> </thead> </table></p> <p> All data are available from the UCSC download servers. For information on how to download specific assembly data, refer to the assembly gateway page once the hub is connected, e.g. -<a href="../../cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCA_004115265.2_mRhiFer1_v1.p" +<a href="../../cgi-bin/hgGateway?hubUrl=https://hgdownload.gi.ucsc.edu/hubs/VGP/hub.txt&genome=GCA_004115265.2_mRhiFer1_v1.p" target="_blank">greater horseshoe bat</a>. This page also includes information on starting a local BLAT server for the assembly.</p> <p> We would like to thank the <a href="https://vertebrategenomesproject.org/" target="_blank">Vertebrate Genomes Project</a> and the <a href="https://genome10k.soe.ucsc.edu/" target="_blank">Genome 10k Project</a> for their sequencing efforts and making these genomes available. We would also like to thank Hiram Clawson and Luis Nassar from the Genome Browser team for the development and release of these assembly hubs.</p> <a name="061920"></a> <h2>Jun. 19, 2020 Updated Self Chain track for human (GRCh38/hg38)</h2> <p> We have updated the <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chr16&g=chainSelf"> Self Chain</a> track for the human GRCh38/hg38 assembly. The Self Chain track shows alignments of the human genome with itself, using a gap scoring system that allows longer @@ -8395,54 +8395,54 @@ <p> We are pleased to announce new NCBI RefSeq assembly hubs for vertebrate genomes. Currently these hubs contain 295 assemblies, encompassing most RefSeq vertebrate genomes.</p> <p> All assemblies contain multiple gene models including NCBI RefSeq annotations, and Ensembl gene predictions where available. Additional tracks include repeat masking and simple repeat data. A complete list of available tracks for each assembly can be found in the respective track statistics pages.</p> <p> The assemblies are divided into five categories. See the assembly statistics link below for a complete list of available genomes in each hub. Assembly statistics such as genome size, gaps, and masking are also available for each genome. Lastly, track statistics are also available displaying all available tracks for each assembly, as well as their genomic coverage.</p><br> <ul> -<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/primates/index.html"> +<li><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/primates/index.html"> </b>Primates</b></a> - <a target="_blank" -href="https://hgdownload.soe.ucsc.edu/hubs/primates/asmStats.html">Assembly statistics</a> -- <a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/primates/trackData.html"> +href="https://hgdownload.gi.ucsc.edu/hubs/primates/asmStats.html">Assembly statistics</a> +- <a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/primates/trackData.html"> Track statistics</a></li> -<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/mammals/index.html"> +<li><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/mammals/index.html"> </b>Mammals</b></a> - <a target="_blank" -href="https://hgdownload.soe.ucsc.edu/hubs/mammals/asmStats.html">Assembly statistics</a> -- <a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/mammals/trackData.html"> +href="https://hgdownload.gi.ucsc.edu/hubs/mammals/asmStats.html">Assembly statistics</a> +- <a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/mammals/trackData.html"> Track statistics</a></li> -<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/birds/index.html"> +<li><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/birds/index.html"> </b>Birds</b></a> - <a target="_blank" -href="https://hgdownload.soe.ucsc.edu/hubs/birds/asmStats.html">Assembly statistics</a> -- <a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/birds/trackData.html"> +href="https://hgdownload.gi.ucsc.edu/hubs/birds/asmStats.html">Assembly statistics</a> +- <a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/birds/trackData.html"> Track statistics</a></li> -<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/fish/index.html"> +<li><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/fish/index.html"> </b>Fish</b></a> - <a target="_blank" -href="https://hgdownload.soe.ucsc.edu/hubs/fish/asmStats.html">Assembly statistics</a> -- <a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/fish/trackData.html"> +href="https://hgdownload.gi.ucsc.edu/hubs/fish/asmStats.html">Assembly statistics</a> +- <a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/fish/trackData.html"> Track statistics</a></li> -<li><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/vertebrate/index.html"> +<li><a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/vertebrate/index.html"> </b>Other vertebrates</b></a> - <a target="_blank" -href="https://hgdownload.soe.ucsc.edu/hubs/vertebrate/asmStats.html">Assembly statistics</a> -- <a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/vertebrate/trackData.html"> +href="https://hgdownload.gi.ucsc.edu/hubs/vertebrate/asmStats.html">Assembly statistics</a> +- <a target="_blank" href="https://hgdownload.gi.ucsc.edu/hubs/vertebrate/trackData.html"> Track statistics</a></li> </ul> <p> These assemblies can be found on our list of <a target="_blank" href="/cgi-bin/hgHubConnect"> Public Hubs</a>, or by searching for a species by NCBI accession or name directly from the <a target="_blank" href="/cgi-bin/hgGateway">Gateway page</a>.</p> <p> We would like to thank NCBI RefSeq for making these data available. We would also like to thank Hiram Clawson and Lou Nassar for the development and release of these hubs.</p> <a name="052220"></a> <h2>May. 22, 2020 Updated GENCODE gene tracks: Human V34 (hg19/hg38) - Mouse M25 (mm10) and updated GTEx V8 gene expression track in hg38</h2> @@ -9202,38 +9202,38 @@ <h2>Mar. 17, 2020 New mitochondrial sequence for human (hg19)</h2> <p> We are pleased to announce the release of a patch to the hg19 assembly that will introduce a new mitochondrial sequence, <a href="../../cgi-bin/hgTracks?db=hg19&position=chrMT:4277-5648" target="_blank">chrMT</a>, to the assembly. We used GenBank sequence NC_001807 for chrM in hg19 and earlier, but the sequence preferred by the community is the revised Cambridge Reference Sequence (rCRS), <a href="https://www.ncbi.nlm.nih.gov/nuccore/251831106" target="_blank">NC_012920</a>. The new chrMT is the rCRS, NC_012920. <a href="https://www.ncbi.nlm.nih.gov/grc/help/patches/" target="_blank">Patch sequences</a> from <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_000001405.14" target="_blank">GRCh37.p13</a> have also been added to hg19.</p> <p> More information on how patch sequences are incorporated can be found on the <a href="https://genome-blog.gi.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. The blog post contains details about the new -<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/latest/" +<a href="https://hgdownload.gi.ucsc.edu/goldenPath/hg19/bigZips/latest/" target="_blank">/latest</a> download directory on the downloads server. With the addition of new sequences to hg19, we can expect to see BLAT return more matches to the genome.</p> <p> Also, with these patches, the hg19 genome is not optimal anymore for aligners. So we added an -"<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/analysisSet/" +"<a href="https://hgdownload.gi.ucsc.edu/goldenPath/hg19/bigZips/analysisSet/" target="_blank">analysis set</a>" version of the hg19 genome fasta file to our -<a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/" target="_blank">bigZips</a> +<a href="https://hgdownload.gi.ucsc.edu/goldenPath/hg19/bigZips/" target="_blank">bigZips</a> directory, and indexes for BWA, Bowtie2, and Hisat2.</p> <p> We would like to thank the Genome Reference Consortium for creating the patches to hg19. We would also like to thank Angie Hinrichs and Jairo Navarro at UCSC for implementing and testing the latest patch to hg19.</a> <a name="022720"></a> <h2>Feb. 27, 2020 New NCBI RefSeq Select + MANE track for Human (hg38)</h2> <p> We are pleased to announce a new track, RefSeq Select+MANE, for the <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38&c=chr1&g=refSeqComposite">GRCh38/hg38</a> human assembly. This track is a combination of NCBI transcripts with the <em>RefSeq Select</em> tag, as well as transcripts with the <em>MANE Select</em> tag. The result is a track with a single representative transcript for every protein-coding gene. The track can be found as part of the NCBI RefSeq composite track.</p> @@ -9458,33 +9458,33 @@ While processing the information downloaded from dbSNP, UCSC annotates some properties of interest. These are noted on the item details page, and may be used to include or exclude affected variants. These UCSC notes (currently 26) can be divided into three categories:</p> <ul> <li>Information about ClinVar status, allele frequencies reported by twelve projects, and the presence of other variants at the same genomic position</li> <li>Notes about rare variants or ambiguous nucleotides in the reference genome</li> <li>Indicators that allele frequency data might be incomplete and/or mapping variants across different assemblies had issues with indel differences between assemblies</li> </ul> <h3>Data Access</h3> <p> With the bigDbSnp format, these data will no longer be available as a database table dump. The complete data can be found across two separate files in our download server, a bigBed file -(bigDbSnp) for <a target="_blank" href="http://hgdownload.soe.ucsc.edu/gbdb/hg19/snp/">hg19</a> -and <a target="_blank" href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/">hg38</a>, and a -<a target="_blank" href="http://hgdownload.soe.ucsc.edu/gbdb/hgFixed/dbSnp/">shared secondary +(bigDbSnp) for <a target="_blank" href="http://hgdownload.gi.ucsc.edu/gbdb/hg19/snp/">hg19</a> +and <a target="_blank" href="http://hgdownload.gi.ucsc.edu/gbdb/hg38/snp/">hg38</a>, and a +<a target="_blank" href="http://hgdownload.gi.ucsc.edu/gbdb/hgFixed/dbSnp/">shared secondary details file</a> which holds additional variant details.<p> <p> Additional information including visibility display, a complete list of UCSC notes, and a methods section can be found in the <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38&g=dbSnp153Composite">track description page</a>.</p> <p> We would like to thanks the dbSNP group at NCBI for providing access to these data. We would also like to thank Angie Hinrichs and the UCSC Genome Browser team for their efforts on this release.</p> <a name="112719a"></a> <h2>Nov. 27, 2019 New EPD TSS track for human and mouse</h2> <p> We are pleased to announce the release of the new EPDnew Promoters track for human @@ -9847,75 +9847,75 @@ <li><B>NCBI BioProject ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/bioproject/476474" TARGET="_blank">476474</A></li> <li><B>NCBI BioSample ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/biosample/SAMN09435472" TARGET="_blank">SAMN09435472</A></li> <li><b>Scaffold count: </b>2,979</li> <li><b>Total size: </b>2,971,331,530</li> <li><a href="../goldenPath/credits.html#rhesus_credits" target="_blank" >Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#rhesus_use" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a> and -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/rheMac10/" +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/rheMac10/" target="_blank" >FTP</a></li> - <li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#rhesus" + <li><a href="http://hgdownload.gi.ucsc.edu/downloads.html#rhesus" target="_blank" >Downloads page</a></li> </ul> </p> <a name="082819"></a> <h2>Aug. 28, 2019 Vertebrate Genomes Project assembly hub</h2> <p> -The UCSC Genome Browser is proud to announce its <a href="https://hgdownload.soe.ucsc.edu/hubs/VGP/" +The UCSC Genome Browser is proud to announce its <a href="https://hgdownload.gi.ucsc.edu/hubs/VGP/" target="_blank">Vertebrate Genomes Project assembly hub</a>. The <a href="https://vertebrategenomesproject.org/" target="_blank">Vertebrate Genomes Project (VGP)</a> aims to generate near error-free reference genome assemblies of all 70,000 extant vertebrate species.</p> <p> -As of now, the <a href="https://hgdownload.soe.ucsc.edu/hubs/VGP/" +As of now, the <a href="https://hgdownload.gi.ucsc.edu/hubs/VGP/" target="_blank">VGP assembly hub</a> includes 24 vertebrate assemblies. See our <a -href="https://hgdownload.soe.ucsc.edu/hubs/VGP/asmStatsVGP.html" +href="https://hgdownload.gi.ucsc.edu/hubs/VGP/asmStatsVGP.html" target="_blank">assembly statistics page</a> for specific information (gap counts, masking percent, genome size, etc.) on each individual assembly. All assemblies have a combination of Genome Browser generated data tracks, as well as external data. These include:</p> <ul> <li>Augustus gene predictions on all assemblies, as well as imported NCBI gene predictions when available.</li> <li>A RefSeq mRNAs track which is generated in-house, mapping RefSeq mRNAs from various other organisms to each individual assembly. This track includes origin mRNA species and gene names, which may help to identify genes on the less annotated assemblies.</li> <li>CpG island and GC percent tracks.</li> <li>Repeat masking tracks by both RepeatMasker and WindowMasker + SDust.</li></ul> <p> These tracks also include individual track description pages with a summary of their contents or results where applicable. Such as a summary of all RepeatMasker elements found in the -<a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=hub_1489433_GCA_007474595.1_mLynCan4_v1.p&g=hub_1489433_repeatMasker" +<a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?hubUrl=https://hgdownload.gi.ucsc.edu/hubs/VGP/hub.txt&genome=hub_1489433_GCA_007474595.1_mLynCan4_v1.p&g=hub_1489433_repeatMasker" target="_blank">Canada lynx</a> or gene count and genome coverage of NCBI genes for the -<a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=hub_1489433_GCF_004115215.1_mOrnAna1.p.v1&g=hub_1489433_ncbiGene" +<a href="https://genome.ucsc.edu/cgi-bin/hgTrackUi?hubUrl=https://hgdownload.gi.ucsc.edu/hubs/VGP/hub.txt&genome=hub_1489433_GCF_004115215.1_mOrnAna1.p.v1&g=hub_1489433_ncbiGene" target="_blank">platypus</a>.</p> <p> All data are available from the UCSC download servers. For information on how to download specific assembly data, refer to the assembly gateway page once the hub is connected. Here is an example of the gateway page for the -<a href="../../cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/VGP/hub.txt&genome=GCA_004115265.2_mRhiFer1_v1.p" +<a href="../../cgi-bin/hgGateway?hubUrl=https://hgdownload.gi.ucsc.edu/hubs/VGP/hub.txt&genome=GCA_004115265.2_mRhiFer1_v1.p" target="_blank">greater horseshoe bat</a>. This page also includes information on starting a local BLAT server for the assembly.</p> <p> We would like to thank the <a href="https://vertebrategenomesproject.org/" target="_blank">Vertebrate Genomes Project</a> and the <a href="https://genome10k.soe.ucsc.edu/" target="_blank">Genome 10k Project</a> for their sequencing efforts and making these genomes available. We would also like to thank Hiram Clawson and Luis Nassar from the Genome Browser team for the development and release of this assembly hub.</p> <a name="073119"></a> <h2>Jul. 31, 2019 New Genome Browser: Horse, equCab3 (<em>Equus caballus</em>)</h2> <p> A genome browser is now available for the <em>Equus caballus</em> assembly released in Jan. 2018 by the <a href="https://louisville.edu/medicine/" target="_blank"> University of Louisville</a> (EquCab3.0). @@ -9934,33 +9934,33 @@ <li><b>NCBI BioProject ID:</b> <a href="https://www.ncbi.nlm.nih.gov/bioproject/421018" target="_blank">421018</a></li> <li><b>NCBI BioSample ID:</b> <a href="https://www.ncbi.nlm.nih.gov/biosample/SAMN02953672" target="_blank">SAMN02953672</a></li> <li><b>Scaffold count: </b>4,701</li> <li><b>Total size: </b>2,506,966,135</li> <li><a href="../goldenPath/credits.html#horse_credits" target="_blank" >Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#horse_use" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a> and -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/equCab3/" +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/equCab3/" target="_blank" >FTP</a></li> - <li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#horse" + <li><a href="http://hgdownload.gi.ucsc.edu/downloads.html#horse" target="_blank" >Downloads page</a></li> </ul> </p> <a name="071919"></a> <h2>Jul. 19, 2019 New GENCODE V31 gene tracks for human, hg19 and hg38</h2> <p> We are pleased to announce the release of the new GENCODE Gene annotation tracks, which corresponds to the <a href="http://www.ensembl.info/2019/05/20/whats-coming-in-ensembl-97-ensembl-genomes-44/" target="_blank">Ensembl 97 release</a> for human assemblies, <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencodeV31lift37">hg19/GRCh37</a> and <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38&g=wgEncodeGencodeV31">hg38/GRCh38</a>. All GENCODE V31 annotations are available for hg38/GRCh38, and the annotation release was back-mapped to the hg19/GRCh37 assembly. For both hg19 and hg38, the GENCODE v31 gene set contains the following tracks:</p> @@ -10006,31 +10006,31 @@ <p> The TransMap tracks are an attempt to map features, such as mRNAs, ESTs, and gene annotations from one organism to another through pairwise, whole-genome alignments. These new TransMap tracks are:</p> <ul> <li>Ensembl Mappings</li> <li>RefSeq Gene Mappings</li> <li>GenBank RNA Mappings</li> <li>EST Mappings</li> </ul> <p> You can read more about how these tracks were created on the <a href="../../cgi-bin/hgTrackUi?db=hg38&g=transMapV5" target="_blank">track description page</a> for the hg38/GRCh38 version of these tracks. The TransMapV4 data can still be found in our -<a href="http://hgdownload.soe.ucsc.edu/gbdb/" target="_blank">download server</a>.</p> +<a href="http://hgdownload.gi.ucsc.edu/gbdb/" target="_blank">download server</a>.</p> <p> Thanks to Mark Diekhans and Lou Nassar for their work in creating and releasing these tracks.</p> <a name="070919"></a> <h2>Jul. 9, 2019 Expanded CRISPR track released for human (hg19/GRCh37)</h2> <p> We are pleased to announce the release of an expanded <a href="../cgi-bin/hgTracks?db=hg19&hideTracks=1&knownGene=pack&crisprAllTargets=pack&position=chr7:116397500-116398000" target="_blank">CRISPR Targets track</a> for the human hg19/GRCh37 assembly. This track shows the DNA sequences targetable by CRISPR RNA guides using the Cas9 enzyme from <i>S. pyogenes</i> (PAM: NGG) over the entire human genome. CRISPR target sites were annotated with predicted specificity (off-target effects) and predicted efficiency (on-target cleavage) by various algorithms through the tool <a href="http://crispor.tefor.net/" target="_blank">CRISPOR</a>. </p> @@ -10114,37 +10114,37 @@ <li><B>NCBI BioProject ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/bioproject/54005" TARGET="_blank">54005</A></li> <li><B>NCBI BioSample ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/biosample/SAMN02981400" TARGET="_blank">SAMN02981400</A></li> <li><b>Scaffold count: </b>71,135</li> <li><b>Total size: </b>2,959,373,024</li> <li><a href="../goldenPath/credits.html#Baboon_credits" target="_blank" >Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a></li> - <li>FTP: <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/" + <li>FTP: <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/bosTau9/" target="_blank" >Cow</a> and -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/papAnu4/" +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/papAnu4/" target="_blank" >Baboon</a></li> - <li>Downloads page: <a href="http://hgdownload.soe.ucsc.edu/downloads.html#cow" + <li>Downloads page: <a href="http://hgdownload.gi.ucsc.edu/downloads.html#cow" target="_blank" >Cow</a> and -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#baboon" +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#baboon" target="_blank" >Baboon</li> </ul> </p> <a name="062519"></a> <h2> Jun. 25, 2019 JSON API now available</h2> <p> The UCSC Genome Browser is pleased to announce its new <a href="help/api.html" target="_blank">JavaScript Object Notation (JSON) Application Programming Interface (API)</a>. The API provides direct access to different data including annotations and sequence data for both native Genome Browser assemblies as well as hubs.</p> <p> Some functions possible with the API include: @@ -10277,33 +10277,33 @@ <li><b>NCBI BioProject information:</b><a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJEB21211" target="_blank" > PRJEB21211</a></li> <li><b>NCBI BioSample information:</b><a href="https://www.ncbi.nlm.nih.gov/biosample/SAMEA104116709" target="_blank" > SAMEA104116709</a></li> <li><b>Contig+scaffold count:</b> 71,598</li> <li><b>Total size:</b> 2,358,908,658</li> <li><a href="../goldenPath/credits.html#chinese_hamster_credits" target="_blank" >Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#chinese_hamster_use" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a> and -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/criGriChoV2/" +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/criGriChoV2/" target="_blank" >FTP</a></li> - <li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#chinese_hamster" + <li><a href="http://hgdownload.gi.ucsc.edu/downloads.html#chinese_hamster" target="_blank" >Downloads page</a></li> </ul> </p> <a name="052119"></a> <h2>May 21, 2019 New Genome Browser: Cat, felCat9 (<em>Felis catus</em>)</h2> <p> A genome browser is now available for the <em>Felis catus</em> assembly released in November 2017 by the <a href="https://www.genome.wustl.edu/" target="_blank">Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine</a> (Felis_catus_9.0). <h3>About the assembly:</h3> <ul> <li><b>UCSC Genome Browser assembly ID:</b> felCat9</li> <li><b>Sequencing/Assembly provider ID:</b> <a href="https://www.genome.wustl.edu/" target="_blank"> Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine</a></li> <li><b>Assembly date:</b> November 2017</li> @@ -10315,33 +10315,33 @@ <li><b>NCBI BioProject information:</b><a href="https://www.ncbi.nlm.nih.gov/bioproject/16726" target="_blank" > 16726</a></li> <li><b>NCBI BioSample information:</b><a href="https://www.ncbi.nlm.nih.gov/biosample/SAMN02953640" target="_blank" > SAMN02953640</a></li> <li><b>Contig+scaffold count:</b> 9434</li> <li><b>Total size:</b> 2,521,863,845</li> <li><a href="../goldenPath/credits.html#cat_credits" target="_blank" >Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#cat_use" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a> and -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/felCat9/" +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/felCat9/" target="_blank" >FTP</a></li> - <li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#cat" + <li><a href="http://hgdownload.gi.ucsc.edu/downloads.html#cat" target="_blank" >Downloads page</a></li> </ul> </p> <a name="041019"></a> <h2>Apr. 10, 2019 GENCODE Genes VM20 track released for mouse (GRCm38/mm10)</h2> <p> We are pleased to announce the release of the GENCODE Genes VM20 track for the Mouse assembly (<a href="../cgi-bin/hgTracks?db=mm10&position=chr12%3A56694976-56714605&hideTracks=1&knownGene=full&ignoreCookie=1" target="_blank">GRCm38/mm10</a>). In this GENCODE Genes update, we have made the ENSMUST* IDs the default IDs and have added the GENCODE pseudogenes to the knownGene tables. </p> @@ -10718,33 +10718,33 @@ <li><b>NCBI BioProject information:</b><a href="https://www.ncbi.nlm.nih.gov/bioproject/13342" target="_blank" > 13342</a></li> <li><b>NCBI BioSample information:</b><a href="https://www.ncbi.nlm.nih.gov/biosample/SAMN02981218" target="_blank" > SAMN02981218</a></li> <li><b>Contig+scaffold count:</b> 1928</li> <li><b>Total size:</b> 1,065,365,425</li> <li><a href="../goldenPath/credits.html#chicken_credits" target="_blank" >Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#chicken_use" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a> and -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/galGal6/" +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/galGal6/" target="_blank" >FTP</a></li> - <li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#chicken" + <li><a href="http://hgdownload.gi.ucsc.edu/downloads.html#chicken" target="_blank" >Downloads page</a></li> </ul> </p> <a name="111918"></a> <h2>Nov. 19, 2018 New Genome Browser: Orangutan, ponAbe3 (<em>Pongo pygmaeus abelii </em>)</h2> <p> A genome browser is now available for the <em>Pongo pygmaeus abelii</em> assembly released in January 2018 by the <a href="http://www.gs.washington.edu/" target="_blank"> University of Washington</a> (Susie_PABv2). <h3>About the assembly:</h3> <ul> <li><b>UCSC Genome Browser assembly ID:</b> ponAbe3</li> <li><b>Sequencing/Assembly provider ID:</b> <a href="http://eichlerlab.gs.washington.edu/index.html"> University of Washington</a></li> @@ -10757,33 +10757,33 @@ <li><b>NCBI BioProject information:</b><a href="https://www.ncbi.nlm.nih.gov/bioproject/369439" target="_blank" > 369439</a></li> <li><b>NCBI BioSample information:</b><a href="https://www.ncbi.nlm.nih.gov/biosample/SAMN06275555" target="_blank" > SAMN06275555</a></li> <li><b>Contig+scaffold count:</b> 5,300</li> <li><b>Total size:</b> 3,065,052,215</li> <li><a href="../goldenPath/credits.html#orangutan_credits" target="_blank" >Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#orangutan_use" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a> and -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/ponAbe3/" +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/ponAbe3/" target="_blank" >FTP</a></li> - <li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#orangutan" + <li><a href="http://hgdownload.gi.ucsc.edu/downloads.html#orangutan" target="_blank" >Downloads page</a></li> </ul> </p> <a name="111618"></a> <h2>Nov. 16, 2018 GENCODE Genes v29 track released for human (GRCh38/hg38)</h2> <p> We are pleased to announce the release of the GENCODE Genes v29 track for the Human (<a href="../cgi-bin/hgGateway?db=hg38" target="_blank">GRCh38/hg38</a>) assembly. In this GENCODE Genes update, we have made the ENST* IDs the default IDs and have added the GENCODE pseudogenes to the knownGene tables. </p> <p> More details about the GENCODE Genes v29 track can be found on the <a href="../cgi-bin/hgTrackUi?db=hg38&g=knownGene" target="_blank">GENCODE Genes track description @@ -10922,32 +10922,32 @@ <a href="https://www.ncbi.nlm.nih.gov/assembly/305108" target="_blank">anoGam3</a>. </li> </ul> <h3>Garter snake <a href="../cgi-bin/hgGateway?db=thaSir1">(Thamnophis_sirtalis-6.0/thaSir1)</a> </h3> <ul> <li>Assembly released Jun. 2015 by <a href="https://www.genome.wustl.edu/" target="_blank">The Genome Institute at Washington University School of Medicine</a>.</li> <li>There are 7,930 scaffolds with a total size of 1,424,897,867 bases.</li> <li>For more information about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/472161" target="_blank">thaSir1</a>.</li> </ul> <p> Bulk downloads of the sequence and annotation data may be obtained from the -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/">Genome Browser FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html">Downloads page</a>. Please observe the +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/">Genome Browser FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html">Downloads page</a>. Please observe the <a href="https://genome.ucsc.edu/FAQ/FAQdownloads.html#download2">conditions of use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="https://genome.ucsc.edu/goldenPath/credits.html">Credits</a> for a detailed list of the organizations and individuals who contributed to these releases.</p> <a name="081018"></a> <h2>Aug. 10, 2018 New interact track type</h2> <p> The UCSC Genome Browser is proud to announce a new method to visualize interactions between regions of the genome. The interact track format (and the binary-indexed bigInteract version) displays pairwise interactions as arcs or half-rectangles connecting two genomic regions on the same chromosome. Cross-chromosomal interactions can also be represented in this format. This format is useful for displaying functional element interactions such as SNP/gene interactions, and is also suitable for low-density chromatin interactions, such as ChIA-PET, and other use cases with a @@ -11327,32 +11327,32 @@ <li><b>NCBI Assembly information:</b><a href="https://www.ncbi.nlm.nih.gov/assembly/1474531" target="_blank"> 1474531</a> <em> (Pmar_germline 1.0) </em></li> <li><b>BioProject information:</b><a href="https://www.ncbi.nlm.nih.gov/bioproject/357048" target="_blank"> 357048</a></li> <li><b>BioSample information:</b><a href="https://www.ncbi.nlm.nih.gov/biosample/SAMN06131802" target="_blank"> SAMN06131802</a></li> <li><b>Contig+scaffold count:</b> 36,453</li> <li><b>Total size:</b> 1,130,417,696</li> <li><a href="../goldenPath/credits.html#lamprey_credits" target="_blank">Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#lamprey_use" target="_blank"> Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank">Rsync</a> and - <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/petMar3/" target="_blank">FTP</a></li> - <li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#lamprey" target="_blank"> + <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/petMar3/" target="_blank">FTP</a></li> + <li><a href="http://hgdownload.gi.ucsc.edu/downloads.html#lamprey" target="_blank"> Downloads page</a></li> </ul> <a name="022018"></a> <h2>Feb. 20, 2018 New video: Visibility control in the Browser </h2> <p> We have released a new video demonstrating the <a href="https://www.youtube.com/watch?v=jKix2B3hwnw&list=UUQnUJepyNOw0p8s2otX4RYQ" target=_blank>visibility controls</a> in the Browser. In our Browser <a href = "http://bit.ly/ucscTraining" target = _blank>training workshops</a> we are often asked about the meaning of the track controls: squish, dense, pack and full. In this tutorial we describe the controls for BED, wiggle and conservation tracks. There is also a discussion of visibility control in composite tracks (2-level nesting) and supertracks (3-level). @@ -11745,33 +11745,33 @@ <li><b>BioProject information:</b><a href="https://www.ncbi.nlm.nih.gov/bioproject/169343" target="_blank" > NCBI Bioproject: 169343</a></li> <li><b>BioSample information:</b><a href="https://www.ncbi.nlm.nih.gov/biosample/SAMEA1029457" target="_blank" > NCBI Biosample: SAMEA1029457</a></li> <li><b>Contig+scaffold count:</b> 132,340</li> <li><b>Total size:</b> 3,286,643,896</li> <li><a href="../goldenPath/credits.html#bonobo_credits" target="_blank">Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#bonobo_use" target="_blank">Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank">Rsync</a> and -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/panPan2/" +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/panPan2/" target="_blank">FTP</a></li> -<li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#bonobo" +<li><a href="http://hgdownload.gi.ucsc.edu/downloads.html#bonobo" target="_blank">Downloads page</a></li> </ul> <a name="121317"></a> <h2>Dec. 13, 2017 New NCBI RefSeq Functional Elements tracks for human and mouse</h2> <p> We are pleased to announce the release of a new set of <a href="https://www.ncbi.nlm.nih.gov/refseq/functionalelements/" target="_blank">functional regulatory elements</a> for the <a href="../cgi-bin/hgTrackUi?db=hg38&g=refSeqFuncElems" target="_blank">hg38/GRCh38</a> and <a href="../cgi-bin/hgTrackUi?db=mm10&g=refSeqFuncElems" target="_blank">mm10/GRCm38</a> assemblies. NCBI is now providing <a href="https://www.ncbi.nlm.nih.gov/refseq/" target="_blank">RefSeq</a> and <a href="https://www.ncbi.nlm.nih.gov/gene/" target="_blank">Gene</a> records for non-genic functional elements that have been described in the literature and are experimentally validated. Elements in scope include experimentally-verified gene regulatory regions, known structural @@ -11848,33 +11848,33 @@ <li><b>BioProject information:</b><a href="https://www.ncbi.nlm.nih.gov/bioproject/12348" target="_blank" > NCBI Bioproject: 12348</a></li> <li><b>BioSample information:</b><a href="https://www.ncbi.nlm.nih.gov/biosample/SAMN00000117" target="_blank" > NCBI Biosample: SAMN00000117</a></li> <li><b>Contig+scaffold count:</b> 68,152</li> <li><b>Total size:</b> 1,440,398,454</li> <li><a href="../goldenPath/credits.html#xentro_credits" target="_blank" >Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#xentro_use" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a> and -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/xenTro9/" +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/xenTro9/" target="_blank" >FTP</a></li> -<li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#xentro" +<li><a href="http://hgdownload.gi.ucsc.edu/downloads.html#xentro" target="_blank" >Downloads page</a></li> </ul> <a name="112117"></a> <h2>Nov. 21, 2017 New NCBI RefSeq tracks for mouse, mm10</h2> <p> We are pleased to announce the release of a new set of gene annotation tracks for the mm10/GRCm38 assembly based on data from NCBI's Reference Sequence Database (RefSeq). For all of these tracks, the alignments and coordinates are provided by RefSeq. These tracks are organized in a composite track that includes:</p> <ul> <li>RefSeq All – all annotations from the curated and predicted sets <li>RefSeq Curated – curated annotations beginning with NM, NR, or NP <li>RefSeq Predicted – predicted annotations beginning with XM or XR <li>RefSeq Other – all other RefSeq annotations not included in RefSeq All @@ -11915,33 +11915,33 @@ <li><b>BioProject information:</b><a href="https://www.ncbi.nlm.nih.gov/bioproject/338693" target="_blank" > NCBI Bioproject: 338693</a></li> <li><b>BioSample information:</b><a href="https://www.ncbi.nlm.nih.gov/biosample/SAMN04518361" target="_blank" > NCBI Biosample: SAMN04518361</a></li> <li><b>Contig/scaffold count: </b>108,033</li> <li><b>Total size:</b> 2,718,433,805</li> <li><a href="../goldenPath/credits.html#african_clawed_frog_credits" target="_blank" >Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#african_clawed_frog_use" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a> and -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/xenLae2/" +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/xenLae2/" target="_blank" >FTP</a></li> -<li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#african_clawed_frog" +<li><a href="http://hgdownload.gi.ucsc.edu/downloads.html#african_clawed_frog" target="_blank" >Downloads page</a></li> </ul> <a name="111317"></a> <h2>Nov. 13, 2017 New genome browser: Pig, susScr11 <em>(Sus scrofa)</em> </h2> <p>Please welcome <a href="../cgi-bin/hgGateway?db=susScr11" target="_blank" >susScr11</a>, the 191st genome assembly in the UCSC Genome Browser. This is the third assembly in the browser for pig <em>(Sus scrofa)</em> .</p> <h3>About the assembly:</h3> <ul> <li><b>UCSC Genome Browser assembly ID:</b> susScr11</li> <li><b>Sequencing/Assembly provider ID:</b> The Swine Genome Sequencing Consortium (SGSC) Sscrofa11.1</li> <li><b>Assembly date:</b> Feb. 2017</li> @@ -11953,33 +11953,33 @@ <li><b>BioProject ID:</b><a href="https://www.ncbi.nlm.nih.gov/bioproject/13421" target="_blank" > 13421</a></li> <li><b>BioSample ID:</b><a href="https://www.ncbi.nlm.nih.gov/biosample/SAMN02953785" target="_blank" > SAMN02953785</a></li> <li><b>Contig/scaffold count: </b>613</li> <li><b>Total size:</b> 2,501,912,388</li> <li><a href="../goldenPath/credits.html#pig_credits" target="_blank" >Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#pig_use" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a> and -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/susScr11/" +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/susScr11/" target="_blank" >FTP</a></li> -<li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#pig" +<li><a href="http://hgdownload.gi.ucsc.edu/downloads.html#pig" target="_blank" >Downloads page</a></li> </ul> <a name="110717"></a> <h2>Nov. 07, 2017 New genome browser: Chinese hamster <em>(Cricetulus griseus)</em> ovary cell line, CHO-K1</h2> <p>Please welcome <a href="../cgi-bin/hgGateway?db=criGriChoV1" target="_blank" >criGriChoV1</a>, the 190th genome assembly in the UCSC Genome Browser. This assembly marks the first cell line to reside in the browser; the Chinese hamster <em>(Cricetulus griseus)</em> ovary cell line, CHO-K1.</p> <h3>About the assembly:</h3> <ul> <li><b>UCSC Genome Browser assembly ID:</b> criGriChoV1</li> <li><b>Sequencing/Assembly provider ID:</b> Beijing Genomics Institute CriGri_1.0</li> <li><b>Assembly date:</b> Aug. 2011</li> @@ -11991,50 +11991,50 @@ <li><b>BioProject ID:</b><a href="https://www.ncbi.nlm.nih.gov/bioproject/69991" target="_blank" > 69991</a></li> <li><b>BioSample ID:</b><a href="https://www.ncbi.nlm.nih.gov/biosample/SAMN02981352" target="_blank" > SAMN02981352</a></li> <li><b>Contig/scaffold count: </b>109,152</li> <li><b>Total size:</b> 2,399,786,748</li> <li><a href="../goldenPath/credits.html#chinese_hamster_credits" target="_blank" >Acknowledgments</a></li> </ul> <h3>Data and Downloads:</h3> <ul> <li><a href="../goldenPath/credits.html#chinese_hamster_use" target="_blank" >Data use conditions and restrictions</a></li> <li><a href="../goldenPath/help/ftp.html" target="_blank" >Rsync</a> and -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/criGriChoV1/" +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/criGriChoV1/" target="_blank" >FTP</a></li> -<li><a href="http://hgdownload.soe.ucsc.edu/downloads.html#chinese_hamster" +<li><a href="http://hgdownload.gi.ucsc.edu/downloads.html#chinese_hamster" target="_blank" >Downloads page</a></li> </ul> <a name='110217'></a> <h2>Nov. 2, 2017 New Zebrafish assembly danRer11 available!</h2> <p> A genome browser is now available for the Zebrafish (<em>Danio rerio</em>) assembly released in May 2017 by The Genome Reference Consortium. For more information and statistics about this assembly, see the <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.6/"> NCBI assembly record</a> for GRCz11. There are 20,680 contigs and 2,848 scaffolds in this assembly with a total size of 1,679,203,469 bases. </p> <p> Bulk downloads of the sequence and annotation data may be obtained from the <a -href="ftp://hgdownload.soe.ucsc.edu/goldenPath/danRer11">Genome Browser FTP -server</a> or the <a href="http://hgdownload.soe.ucsc.edu/downloads.html#zebrafish">Downloads +href="ftp://hgdownload.gi.ucsc.edu/goldenPath/danRer11">Genome Browser FTP +server</a> or the <a href="http://hgdownload.gi.ucsc.edu/downloads.html#zebrafish">Downloads page</a>. Please observe the <a href="https://genome.ucsc.edu/FAQ/FAQdownloads.html#download2"> conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#zebrafish_credits">Credits page</a> for a detailed list of the organizations and individuals who contributed to this release. </p> <a name="102717"></a> <h2>Oct. 27, 2017 Public European UCSC MariaDB server now available!</h2> <p> We are pleased to announce that a public MariaDB server of UCSC Genome Browser data is now available in Europe! This should speed up programmatic access to the underlying MariaDB databases for users in Europe. Connect to this new MariaDB server using the command:</p> <pre><code> mysql --user=genome --host=genome-euro-mysql.soe.ucsc.edu -A</code></pre> @@ -12079,41 +12079,41 @@ <p> <b><a href="../cgi-bin/hgTrackUi?db=hg19&g=gtexEqtlTissue" target="_blank">hg19: GTEx Tissue eQTL </a></b></br>This track is a composite track containing 44 subtracks representing the GTEx eQTL tissues. Each subtrack contains all eQTLs identified for that tissue. Filtering is available for all 44 subtracks.</p> <p> These two tracks join the previously released GTEx data tracks and track hubs in the UCSC Genome Browser: <ul> <li><a href="../cgi-bin/hgGtexTrackSettings?db=hg19&g=gtexGene" target="_blank">GTEx Gene</a></li> <li><a href="../cgi-bin/hgTrackUi?db=hg19&g=gtexTranscExpr" target="_blank"> GTEx Transcript</a></li> -<li><a href="http://hgdownload.soe.ucsc.edu/hubs/gtex/gtexHub.html" target="_blank"> +<li><a href="http://hgdownload.gi.ucsc.edu/hubs/gtex/gtexHub.html" target="_blank"> GTEx RNA-Seq Signal Hub</a> on <a href=" -../cgi-bin/hgTracks?db=hg38&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt" +../cgi-bin/hgTracks?db=hg38&hubUrl=http://hgdownload.gi.ucsc.edu/hubs/gtex/hub.txt" target="_blank">hg19</a> and -<a href="../cgi-bin/hgTracks?db=hg38&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt" +<a href="../cgi-bin/hgTracks?db=hg38&hubUrl=http://hgdownload.gi.ucsc.edu/hubs/gtex/hub.txt" target="_blank">hg38</a>.</li> -<li><a href="http://hgdownload.soe.ucsc.edu/hubs/gtexAnalysis/gtexAse.html" target="_blank"> +<li><a href="http://hgdownload.gi.ucsc.edu/hubs/gtexAnalysis/gtexAse.html" target="_blank"> GTEx Analysis Hub: Allele-Specific Expression</a> on <a href=" ../cgi-bin/hgTracks?db=hg38&hubUrl= -http://hgdownload.soe.ucsc.edu/hubs/gtexAnalysis/gtexAnalysisHub.html" target="_blank">hg19</a> and -<a href="../cgi-bin/hgTracks?db=hg38&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtexAnalysis/gtexAnalysisHub.html" +http://hgdownload.gi.ucsc.edu/hubs/gtexAnalysis/gtexAnalysisHub.html" target="_blank">hg19</a> and +<a href="../cgi-bin/hgTracks?db=hg38&hubUrl=http://hgdownload.gi.ucsc.edu/hubs/gtexAnalysis/gtexAnalysisHub.html" target="_blank">hg38</a>.</li> </ul> <p> Please see the related October 11, 2017 publication in <i>Nature</i>, "<a href="https://www.nature.com/nature/journal/v550/n7675/full/nature24277.html" target="_blank">Genetic effects on gene expression across human tissues</a>" for an in-depth article about these data.</p> <p> Acknowledgments to UCSC Genome Browser engineer, Kate Rosenbloom, for creating these tracks. </p> <a name="092917"></a> <h2>Sep. 29, 2017 VAI tool can now output HGVS terms</h2> @@ -12298,31 +12298,31 @@ href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>.</p> <!-- above address is genome at soe.ucsc.edu --> <p> We would like to thank Hiram Clawson, Maximilian Haeussler, Christopher Lee, and Jairo Navarro for the development and release of these tracks.</p> <a name="071417"></a> <h2>Jul. 14, 2017 New alternative mouse strain hub and strain-specific annotations</h2> <p> A mouse strain assembly hub is now available and shows an alignment of 16 assembled laboratory mice strains, including the reference mouse (mm10) as well as the reference rat (rn6). This hub contains some of the most common mice strains used in disease models such as NOD, BALB/c, and C3H. Each mouse strain in the assembly hub is displayed as the primary sequence along with strain-specific annotations. You can load this hub from our <a href="../cgi-bin/hgHubConnect" target="_blank">Public Hubs</a> or the following -<a href="http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hubIndex.html" target="_blank">page</a>. +<a href="http://hgdownload.gi.ucsc.edu/hubs/mouseStrains/hubIndex.html" target="_blank">page</a>. </p> <p> Along with the release of this assembly hub, a new track is available for mm10. The <a href="../cgi-bin/hgTrackUi?db=mm10&g=strainSNPs" target="_blank">Mouse SNPs</a> track shows single nucleotide variants between the different strains of mice and all SNP and indel calls are relative to the reference mouse genome (GRCm38/mm10).</p> <p> Special thanks to Joel Armstrong, Ian Fiddles, and Benedict Paten for the alignment generation, as well as Thomas Keane and the <a href="http://www.sanger.ac.uk/science/data/mouse-genomes-project" target="_blank">Mouse Genomes Project</a> for providing the genome assemblies. Thanks to Hiram Clawson and Jairo Navarro for the development and release of this track and hub.</p> <a name="2017-07-14"></a> <h2>Jul. 14, 2017 New Video: Multi-Region mode for viewing discontinuous regions in the Browser</h2> @@ -12402,31 +12402,31 @@ how you can get boxplots of data points to show up on track item <a href="../../cgi-bin/hgc?db=hg38&c=chr9&l=133255601&r=133275214&o=133257408&t=133275201&g=gtexGene&i=ABO"> details pages</a>? Well, look no further as we have just released support for a GTEx style <a href="help/barChart.html">barChart track format</a>. This new track format is available for use with custom tracks, and in binary format (bigBarChart) for use in track hubs. Both barChart and bigBarChart formats support external matrix and sample files specifying data points for a boxplot display on details pages, while the barChart/bigBarChart file typically specifies summary values (mean or median) over the matrix, which determines the bar heights. See the <a href="help/barChart.html">documentation</a> for further explanation and examples. </p> <p> Along with the release of this new track format are some tools that help to create the tracks, <code>expMatrixToBarchartBed</code> and <code>bedJoinTabOffset</code>. Both utilities are free for -all use cases, and can be downloaded from our <a href="http://hgdownload.soe.ucsc.edu/admin/exe"> +all use cases, and can be downloaded from our <a href="http://hgdownload.gi.ucsc.edu/admin/exe"> directory of utilities</a>. For more information about this new track format and helper scripts, please see the <a href="help/barChart.html">help documentation</a>. </p> <p> Thanks to Kate Rosenbloom, Christopher Eisenhart and Christopher Lee for the development and testing of this new track format. </p> <a name="060817"></a> <h2>Jun. 8, 2017 New command line tool for annotating variants, vai.pl</h2> <p> We are pleased to announce the release of a new command-line tool for annotating variants, <code>vai.pl</code>. This program is similar to our web-based <a href="../../cgi-bin/hgVai">Variant Annotation Integrator (VAI)</a>, except it allows for bypassing @@ -12446,64 +12446,64 @@ Thanks to Angie Hinrichs and Christopher Lee for the development and testing of the program.</p> <a name="060617"></a> <h2>Jun. 6, 2017 New genome browser available for ciona intestinalis</h2> <p> A genome browser is now available for the ciona intestinalis(<em>vase tunicate</em>) assembly released in April 2011 by The Graduate School of Science, Kyoto University. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000224145.1/" target="_blank"> Ciona intestinalis</a>. There are 6,381 contigs and 1,272 scaffolds in this assembly with a total size of 115,227,500 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/ci3/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#ciona">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/ci3/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#ciona">Downloads</a> page. Please observe the <a href="credits.html#ciona">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#ciona_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="060217"></a> <h2>Jun. 2, 2017 New default tracks for human and mouse assemblies</h2> <p> We have made several changes to the sets of default tracks for some of our human and mouse assemblies. The <a href="https://genome-blog.gi.ucsc.edu/blog/gtex-resources-in-the-browser/" target="_blank">GTEx Gene Expression</a> track is now part of the set of default tracks for both human genome assemblies hg38 and hg19. In addition, we have added the <a href="../../cgi-bin/hgTrackUi?db=hg19&g=dgvPlus">DGV Struct Var</a> track, which displays large structural variant such as CNVs, inversions and in/dels, to the default track set for the human genome assembly hg19. Lastly, for the mouse genome assembly mm10, we have added the <a href="../../cgi-bin/hgTrackUi?db=mm10&g=cons60way">60-way Vertebrate Conservation</a> track to its set of default tracks.</p> <a name="051617"></a> <h2>May 16, 2017 New genome browser available for golden eagle</h2> <p> A genome browser is now available for the golden eagle (<em>Aquila chrysaetos canadensis</em>) assembly released in October 2014 by Washington University. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_000766835.1/" target="_blank">Aquila_chrysaetos-1.0.2</a>. There are 17,032 contigs and 1,142 scaffolds in this assembly with a total size of 1,192,743,076 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/aquChr2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#golden_eagle">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/aquChr2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#golden_eagle">Downloads</a> page. Please observe the <a href="credits.html#golden_eagle_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#golden_eagle_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="051517"></a> <h2>May 15, 2017 New TransMap annotation tracks released</h2> <p>We are pleased to announce the release of a new set of TransMap V4 tracks for nearly 70 different assemblies.</p> <p> The TransMap tracks are an attempt to map features, such as mRNAs, ESTs,and gene predictions from one organism to another through pairwise, whole-genome alignments. These new TransMap tracks are: <ul> @@ -12585,69 +12585,69 @@ <img src="../images/highlightScreenshot2017.png" alt="Highlight screenshot" width="899" height="602"></p> <a name="042117"></a> <h2>Apr. 21, 2017 New Genome Browser available for Chinese pangolin</h2> <p> A Genome Browser is now available for the Chinese pangolin (<em>Manis pentadactyla</em>) assembly released in August 2014 by Washington University. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_000738955.1/" target="_blank">M_pentadactyla-1.1.1</a>. There are 230,930 contigs and 92,772 scaffolds in this assembly with a total size of 2,204,741,241 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/manPen1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#chinese_pangolin">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/manPen1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#chinese_pangolin">Downloads</a> page. Please observe the <a href="credits.html#chinese_pangolin_credits">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#chinese_pangolin_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="042017"></a> <h2>Apr. 20, 2017 New Genome Browsers available for Tibetan frog and American Bison</h2> <p> A Genome Browser is now available for the Tibetan frog (<em>Nanorana parkeri</em>) assembly released in March 2015 by the Bejing Genomics Institute. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000935625.1/" target="_blank">BGI_ZX_2015</a>. There are 147,513 contigs and 25,188 scaffolds in this assembly with a total size of 2,053,867,363 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/nanPar1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#tibetan_frog">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/nanPar1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#tibetan_frog">Downloads</a> page. Please observe the <a href="credits.html#tibetan_frog_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#tibetan_frog_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <hr> <p> A Genome Browser is now available for the American bison (<em>Bison bison bison</em>) assembly released in October 2014 by U.Maryland. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/genome/8907" target="_blank">Bison_UMD1.0</a>. There are 470,415 contigs and 128,431 scaffolds in this assembly with a total size of 2,828,031,685 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/bisBis1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#bison">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/bisBis1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#bison">Downloads</a> page. Please observe the <a href="credits.html#bison_credits">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#bison_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="032017"></a> <h2>Mar. 20, 2017 20 Species Conservation Track now available on RGSC 6.0/rn6</h2> <p> We are pleased to announce the release of a new Conservation track based on the rat (RGSC 6.0/rn6) assembly. This track shows multiple alignments of 20 vertebrate species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package for all species. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track. For more details, visit the @@ -12679,66 +12679,66 @@ examples to our <a href="help/hgTrackHubHelp.html#Compatibility">help documentation</a> that show how to use hubCheck to test track hub compatibility.</p> <a name="031517a"></a> <h2>Mar. 15, 2017 New Genome Browsers available for Golden Snub-Nosed Monkey, Proboscis Monkey, and Turkey</h2> <p> A Genome Browser is now available for the Golden Snub-Nosed Monkey (<em>Rhinopithecus roxellana</em>) assembly released in October 2014 by Novogene. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000769185.1/" target="_blank">Rrox_v1</a>. There are 196,797 contigs and 135,512 scaffolds in this assembly with a total size of 2,899,552,139 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/rhiRox1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#golden_snub-nosed_monkey">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/rhiRox1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#golden_snub-nosed_monkey">Downloads</a> page. Please observe the <a href="credits.html#golden_snub-nosed_monkey_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#golden_snub-nosed_monkey_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <hr> <p> A Genome Browser is now available for the Proboscis Monkey (<em>Nasalis larvatus</em>) assembly released in November 2014 by the Proboscis Monkey Functional Genome Consortium. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_000772465.1/" target="_blank">Charlie1.0</a>. There are 553,412 contigs and 319,549 scaffolds in this assembly with a total size of 3,011,966,170 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/nasLar1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#proboscis_monkey">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/nasLar1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#proboscis_monkey">Downloads</a> page. Please observe the <a href="credits.html#proboscis_monkey_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#proboscis_monkey_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <hr> <p> A Genome Browser is now available for the Turkey (<em>Meleagris gallopavo</em>) assembly released in November 2014 by the Turkey Genome Consortium. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000146605.2/" target="_blank">Turkey_5.0</a>. There are 296,331 contigs and 233,806 scaffolds in this assembly with a total size of 1,128,339,136 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/melGal5/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#Turkey">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/melGal5/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#Turkey">Downloads</a> page. Please observe the <a href="credits.html#Turkey">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#Turkey">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="030317"></a> <h2>Mar. 3, 2017 New NCBI RefSeq tracks released</h2> <p> We are pleased to announce the release of a new set of gene annotation tracks for the hg38/GRCh38 assembly based on data from NCBI's Reference Sequence Database (RefSeq). For all of these tracks, the alignments and coordinates are provided by RefSeq. These tracks are organized in a composite track that includes:</p> <ul> <li>RefSeq All – all annotations from the curated and predicted sets @@ -12900,64 +12900,64 @@ <p> For example, aliases that now map to chr1 are NC_000001.11, CM000663.2, and 1, so that a hg38 search such as CM000663.2 16,560,000 16,615,000 will be equivalent to chr1 16,560,000 16,615,000.</p> <a name="102416"></a> <h2>Oct. 24, 2016 Genome Browsers for chimpanzee, green monkey and gorilla now available</h2> <p> A Genome Browser is now available for the Chimp (<em>Pan troglodytes</em>) assembly released in May 2016 by the Chimpanzee Sequencing and Analysis Consortium. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/733711" target="_blank">Pan_tro 3.0</a>. There are 26 different chromosomes along with 72,326 contigs and 45,511 scaffolds in this assembly with a total size of 3,231,170,666 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/panTro5/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#chimp">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/panTro5/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#chimp">Downloads</a> page. Please observe the <a href="credits.html#chimp_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#chimp_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <p> A Genome Browser is now available for the Green Monkey (<em>Chlorocebus sabaeus</em>) assembly released in March 2014 by the Vervet Genomics Consortium. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/132581" target="_blank">Chlorocebus_sabeus 1.1</a>. There are 32 different chromosomes along with 162,724 contigs and 2,022 scaffolds in this assembly with a total size of 2,789,656,328 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/chlSab2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#green_monkey">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/chlSab2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#green_monkey">Downloads</a> page. Please observe the <a href="credits.html#green_monkey_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#green_monkey_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <p> A Genome Browser is now available for the Gorilla (<em>Gorilla gorilla gorilla</em>) assembly released in March 2016 by the University of Washington. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/705391" target="_blank">GSMRT3</a>. There are 15,997 contigs, Contig N50 of 10,016,017 in this assembly with a total size of 3,080,414,926 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/gorGor5/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#gorilla">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/gorGor5/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#gorilla">Downloads</a> page. Please observe the <a href="credits.html#gorilla_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#gorilla_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="101716"></a> <h2>Oct. 17, 2016 HGVS nomenclature now supported in the Genome Browser</h2> <p> We are pleased to announce the first release of our support for <a href="http://www.hgvs.org/" target="blank">Human Genome Variation Society</a> (HGVS) nomenclature in the Genome Browser. Navigate directly to individual nucleotides or codons using coordinates in the following formats:</p> <ul> <li>NM_198576.3(AGRN):c.1057C>T</li> <li>NM_198056.2:c.1654G>T</li> @@ -12969,32 +12969,32 @@ The gene-name format uses RefSeq genes to identify the codon. In the next release we will add support for nomenclature describing coding (c.) intron and UTR coordinates as well as insertions, deletions and duplications. </p> <a name="083116"></a> <h2>Aug. 31, 2016 Genome Browser for chicken now available</h2> <p> A Genome Browser is now available for the Chicken (<em>Gallus gallus</em>) assembly released December 2015 by the International Chicken Genome Consortium (ICGC). For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/595851" target="_blank">Gallus_gallus-5.0</a>. There are 36 different chromosomes along with 23,439 contigs/scaffolds in this assembly with a total size of 1,230,258,557 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/galGal5/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#chicken">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/galGal5/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#chicken">Downloads</a> page. Please observe the <a href="credits.html#chicken_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#chicken_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="083016"></a> <p> <h2>Aug. 30, 2016 Allele-specific expression in 53 tissues from GTEx Analysis Hub now available</h2> <p> We are pleased to announce the release of Allele Specific Expression (ASE) data for the human hg19 and hg38 assemblies. ASE data from the <a href="http://tllab.org" target="_blank">Lappalainen Lab</a> at the New York Genome Center is now available in the UCSC Genome Browser as a public track hub. This track hub contains ASE data identified from transcriptome and genotype @@ -13047,32 +13047,32 @@ The tracks were produced at UCSC by Angie Hinrichs and Christopher Lee. We'd like to thank the dbSNP group at NCBI for providing access to these data.</p> <a name="081216"></a> <h2>Aug. 12, 2016 Genome Browser for Malayan flying lemur now available</h2> <p> A Genome Browser is now available for the Malayan flying lemur (<em>Galeopterus variegatus</em>) assembly released June 2014 by <a href="http://genome.wustl.edu/genomes/detail/galeopterus-variegatus/" target="_blank">The Genome Institute at Washington University</a>. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/182621" target="_blank"> G_variegatus-3.0.2</a>. There are 179,514 scaffolds with a total size of 3,187,660,572 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/galVar1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#malayan_flying_lemur">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/galVar1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#malayan_flying_lemur">Downloads</a> page. Please observe the <a href="credits.html#malayan_flying_lemur_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#malayan_flying_lemur_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="063016_2"></a> <h2>Jun. 30, 2016 CRAM files now supported</h2> <p> We are excited to announce the support of <a href="help/cram.html" target="_blank">CRAM</a> files on the Browser!</p> <p> CRAM files, which are more dense than BAM files, use an additional external "reference sequence" file to both compress and decompress the read information. For CRAM tracks to load there is an expectation that the checksum of the reference sequence used to create the CRAM file will be in the CRAM header and be accessible from the @@ -13390,67 +13390,67 @@ The tracks were produced at UCSC by Angie Hinrichs and Matthew Speir. We'd like to thank the dbSNP group at NCBI for providing access to these data.</p> <a name="041516_1"></a> <p> <h2>Apr. 15, 2016 Three new assemblies now available in the Genome Browser</h2> <p> A Genome Browser is now available for the gorilla (<em>Gorilla gorilla gorilla</em>) assembly released December 2014 by the Wellcome Trust Sanger Institute. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/503571" target="_blank">gorGor4</a>. There are 25 complete chromosomes alongside 40,667 scaffolds with a total size of 3,063,362,754 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/gorGor4/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#gorilla">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/gorGor4/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#gorilla">Downloads</a> page. Please observe the <a href="credits.html#gorilla_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#gorilla_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <hr> <p> A Genome Browser is now available for the rhesus monkey (<em>Macaca mulatta</em>) assembly released November 2015 by the <a href="https://www.hgsc.bcm.edu/non-human-primates/rhesus-monkey-genome-project" target="_blank">Baylor College of Medicine Human Genome Sequencing Center</a>. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/2715158" target="_blank"> Mmul_8.0.1</a>. There are 23 complete chromosomes alongside 284,705 scaffolds with a total size of 3,236,224,332 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/rheMac8/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#rhesus">Downloads</a> page. Please observe +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/rheMac8/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#rhesus">Downloads</a> page. Please observe the <a href="credits.html#rhesus_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#rhesus_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <hr> <p> A Genome Browser is now available for the crab-eating macaque (<em>Macaca fascicularis</em>) assembly released June 2013 by the <a href="http://genome.wustl.edu/genomes/detail/macaca-fascicularis/" target="_blank">Genome Sequencing Center at Washington University, St. Louis</a>. For more information about this assembly, see <a href="https://www.ncbi.nlm.nih.gov/assembly/704988" target="_blank">Macaca_fascicularis_5.0</a> in the NCBI Assembly database. There are 22 complete chromosomes alongside 7,579 scaffolds with a total size of 2,946,843,737 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/macFas5/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#crab-eating_macaque">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/macFas5/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#crab-eating_macaque">Downloads</a> page. Please observe the <a href="credits.html#crab-eating_macaque_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#crab-eating_macaque_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="040416"></a> <h2>Apr. 4, 2016 New video shows how to obtain sequence or coordinates for exons. </h2> <p> We have released a new <a href="http://genome.ucsc.edu/training/vids/index.html#vid08" target="_blank">video</a> to our YouTube channel. This newest installment in our effort to share the capabilities of the Genome Browser shows how to use the Table Browser to obtain either the sequences or the coordinates for exons in the genes from a chosen region of the genome.</p> <p> We also want to take this opportuinty to remind you that we offer onsite @@ -13491,49 +13491,49 @@ Table Browser</a>. Simply select "mail card deck" from the "output format" menu, and then enter your name and address on the subsequent page. Please allow 4-6 weeks for delivery.</p> <a name="032116"></a> <h2>Mar. 21, 2016 Genome Browsers for <em>C. elegans</em> and brown kiwi now available</h2> <p> A Genome Browser is now available for the <em>Caenorhabditis elegans</em> assembly released February 2013 by the C. elegans Sequencing Consortium (C. elegans Sequencing Consortium version WBcel235, UCSC version ce11). For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/554278" target="_blank">WBcel235</a>. There are 7 complete chromosomes with a total size of 100,286,401 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/ce11/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#c_elegans">Downloads</a> page. Please observe +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/ce11/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#c_elegans">Downloads</a> page. Please observe the <a href="credits.html#ce_credits">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#ce_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <hr> <p> A Genome Browser is now available for the brown kiwi (<em>Apteryx australis</em>) assembly released June 2015 by the <a href="http://www.eva.mpg.de/index.html" target="_blank">Max-Plank Institute for Evolutionary Anthropology</a> (MPI-EVA version AptMan0, UCSC version aptMan1). For more information and statistics about this assembly, see <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_001039765.1" target="_blank">AptMant0</a> in the NCBI Assembly database. There are 24,719 scaffolds with a total size of 1,523,986,457 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/aptMan1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#brown_kiwi">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/aptMan1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#brown_kiwi">Downloads</a> page. Please observe the <a href="credits.html#brown_kiwi_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#brown_kiwi_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="030816"></a> <h2>Mar. 8, 2016 Combine multiple regions of the Genome Browser into a single visualization</h2> <p> Have you ever wished you could remove all of the intronic or intergenic regions from the Genome Browser display? Have you ever dreamed of being able to visualize multiple far-flung regions of a genome? Well, now you can with the new "multi-region" option in the Genome Browser!</p> <p> The multi-region modes provide four different ways to manipulate the display. @@ -13571,49 +13571,49 @@ <a name="021016"></a> <h2>Feb. 10, 2016 Two new assemblies now available in the Genome Browser</h2> <p> A Genome Browser is now available for the mouse lemur (<em>Microcebus murinus</em>) assembly released May 2015 by the <a href="http://www.broadinstitute.org/scientific-community/science/projects/mammals-models/29-mammals-project" target="_blank">The Broad Institute</a> and the <a href="https://www.hgsc.bcm.edu/non-human-primates/mouse-lemur-genome-project" target="_blank">Baylor College of Medicine Human Genome Sequencing Center</a>. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/329621" target="_blank"> Mmur_2.0</a>. There are 10,311 scaffolds with a total size of 2,438,804,424 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/micMur2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#mouse_lemur">Downloads</a> page. Please +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/micMur2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#mouse_lemur">Downloads</a> page. Please observe the <a href="credits.html#mouse_lemur_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#mouse_lemur_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <hr> <p> A Genome Browser is now available for the platypus (<em>Ornithorhynchus anatinus</em>) assembly released February 2007 by the <a href="http://genome.wustl.edu/genomes/detail/ornithorhynchus-anatinus/" target="_blank">Genome Sequencing Center at Washington University, St. Louis</a>. For more information about this assembly, see <a href="https://www.ncbi.nlm.nih.gov/assembly/237598/" target="_blank"> Ornithorhynchus_anatinus-5.0.1</a> in the NCBI Assembly database. There are 201,525 scaffolds with a total size of 1,996,826,513 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/ornAna2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#platypus">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/ornAna2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#platypus">Downloads</a> page. Please observe the <a href="credits.html#platypus_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#platypus_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="012016"></a> <h2>Jan. 20, 2016 dbSNP 142 available for mm10</h2> <p> Data from dbSNP build 142 is now available for the most recent mouse assembly (mm10/GRCm38). As was the case for previous annotations based on dbSNP data, there are three tracks in this release. One is a track containing all mappings of reference SNPs to the mouse assembly, labeled "All SNPs (142)" The other two tracks are subsets of this track and show different interesting and easily defined subsets of dbSNP: </p> <ul> <li> @@ -13661,47 +13661,47 @@ <!-- ============= 2015 archived news ============= --> <a name="2015"></a> <a name="122115"></a> <p> <h2>Dec. 21, 2015 Two new assemblies now available in the Genome Browser</h2> <p> A Genome Browser is now available for the frog (<em>Xenopus tropicalis</em>) assembly released Sept. 2012 by the <a href="http://genome.jgi.doe.gov/" target="_blank">US DOE Joint Genome Institute (JGI-PGF)</a> (JGI v7.0, UCSC version xenTro7). For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/515038" target="_blank">Xtropicalis_v7</a>. There are 7,728 scaffolds with a total size of 1,437,530,879 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/xenTro7/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#xentro">Downloads</a> page. Please observe +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/xenTro7/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#xentro">Downloads</a> page. Please observe the <a href="credits.html#xentro_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators woldwide. See the <a href="credits.html#xentro_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <hr> <p> A Genome Browser is now available for the cat (<em>Felis catus</em>) assembly released Nov. 2014 by the International Cat Genome Sequencing Consortium (ICGSC version Felis_catus_8.0, UCSC version felCat8). For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/1373248" target="_blank">Felis_catus_8.0</a>. There are 267,625 scaffolds with a total size of 2,641,342,258 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/felCat8/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#cat">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/felCat8/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#cat">Downloads</a> page. Please observe the <a href="credits.html#cat_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators woldwide. See the <a href="credits.html#cat_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="121615"></a> <p> <h2>Dec. 16, 2015 Output from related tables now available in the Data Integrator</h2> <p> In the UCSC Genome Browser database, detailed information on the annotations for many tracks is stored in extra tables. This information can include things such as identifiers in other databases, transcript status, or other descriptive information. You can now obtain data from these related tables in your output from the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>.</p> @@ -13873,32 +13873,32 @@ More details about the new GENCODE Basic track can be found on the <a href="../cgi-bin/hgTrackUi?db=hg38&g=knownGene"> GENCODE Basic track description page</a>.</p> <a name="062615"></a> <h2>Jun. 26, 2015 New bonobo (panPan1) assembly now available in the Genome Browser</h2> <p> We are pleased to announce the release of a Genome Browser for the May 2012 assembly of bonobo, <em>Pan paniscus</em> (Max-Planck Institute panpan1, UCSC version panPan1). The assembly was provided by the <a href="http://www.eva.mpg.de/" target="_blank">Max-Planck Institute for Evolutionary Anthropology</a>. There are 10,867 scaffolds with a total size of 2,869,190,071 bases.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/panPan1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#bonobo">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/panPan1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#bonobo">Downloads</a> page. These data have <a href="credits.html#bonobo_credits">specific conditions for use</a>. The bonobo (panPan1) browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="credits.html#bonobo_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="061215"></a> <h2>Jun. 12, 2015 Data Integrator</h2> <p> Have you ever wished that the Table Browser could associate your custom track items with some other track, while retaining the item names from both? We have released a new tool that can do just that, and more: the Data Integrator.</p> <p> Using the Data Integrator you can select up to five tracks, including custom tracks and hub tracks, and output tab-separated text that contains all the fields from both the first track and the overlapping items from the other track(s). If you need only @@ -13984,32 +13984,32 @@ This new format is available for use in custom tracks and data hubs. For more information about bigGenePred, please see our <a href="help/bigGenePred.html">bigGenePred Track Format help page</a>.</p> <a name="040215b"></a> <h2>Apr. 2, 2015 New tarsier (tarSyr2) assembly now available in the Genome Browser</h2> <p> We are pleased to announce the release of a Genome Browser for the Sep. 2013 assembly of tarsier, <em>Tarsius syrichta</em> (WashU Tarsius_syrichta-2.0.1, UCSC version tarSyr2). The whole genome shotgun assembly was provided by <a href="http://genome.wustl.edu/genomes/detail/tarsius-syrichta/" target="_blank">Washington University</a>. There are 337,189 scaffolds with a total size of 3,453,864,774 bases.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/tarSyr2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#tarsier">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/tarSyr2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#tarsier">Downloads</a> page. These data have <a href="credits.html#tarsier_credits">specific conditions for use</a>. The tarsier (tarSyr2) browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="credits.html#tarsier_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="040215a"></a> <h2>Apr. 2, 2015 New training video</h2> <p> Going crazy counting amino acids? Learn an easier way to find the codon number in our new video. See our <a href="../training/index.html" target="_blank">training page</a> or our <a href="http://bit.ly/genomebrowserYoutube" target=_"blank">YouTube channel</a> for details.</p> <a name="040115"></a> <h2>Apr. 1, 2015 New GRCz10 zebrafish assembly now available</h2> <p> @@ -14018,32 +14018,32 @@ <a href="https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/zebrafish/" target="_blank">Genome Reference Consortium</a>, who took over the improvement and maintenance of the zebrafish genome assembly.</p> <p> The GRCz10 assembly improves upon Zv9 by utilizing optical mapping and additional meiotic mapping to fill gaps with new clone sequence and improve the positioning of assembly components. This has also been supplemented with a new whole genome shotgun assembly WGS31. The result is an assembly with a sequence length of 1.3 Gb in 26 chromosomes and 1,035 scaffolds. For more details about the GRCz10 assembly, see the <a href="https://www.ncbi.nlm.nih.gov/assembly/210611" target="_blank">GRCz10 assembly page</a> or the official <a href="https://www.ncbi.nlm.nih.gov/news/10-08-2014-zebrafish-grcz10-annotated/" target="_blank">GRCz10 announcement</a>.</p> <p> The danRer10 sequence and annotation data can be downloaded from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/danRer10/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#zebrafish">downloads</a> page.</p> +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/danRer10/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#zebrafish">downloads</a> page.</p> <p> We'd like to thank the Genome Reference Consortium for providing this assembly. The UCSC zebrafish Genome Browser was produced by Hiram Clawson, Brian Raney and Steve Heitner. See <a href="../goldenPath/credits.html#zebrafish_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="032015"></a> <p> <h2>Mar. 20, 2015 New visualization option for RepeatMasker</h2> <p> We are excited to announce the release of the new RepeatMasker Visualization track for the hg38 and mm10 assemblies. This new RepeatMasker track displays detailed information that includes the amount of unaligned repeat sequence and lines joining repeat fragments. Additionally, repeats are now colored based on their repeat class. This new RepeatMasker track incorporates a new details page that includes the detailed RepeatMasker output and @@ -14056,78 +14056,78 @@ target="_blank">Institute for Systems Biology</a> and the UCSC Genome Browser. We would like to thank Robert Hubley, Arian Smit, Hiram Clawson, and Matthew Speir for their efforts in creating this track.</p> <a name="030315"></a> <h2>Mar. 3, 2015 Use UDR for quick sizable downloads</h2> <p> The UCSC Genome Browser is pleased to share a download protocol to use when downloading large sets of files from our download servers: <strong>UDR (UDT Enabled Rsync)</strong>. UDR utilizes rsync as the transport mechanism, but sends the data over the UDT protocol, which enables huge amounts of data to be downloaded efficiently over long distances.</p> <p> We now have two identical download servers to better serve your needs. You can use either one: <ul> <li> - <a href="http://hgdownload.soe.ucsc.edu" target="_blank">http://hgdownload.soe.ucsc.edu</a></li> + <a href="http://hgdownload.gi.ucsc.edu" target="_blank">http://hgdownload.gi.ucsc.edu</a></li> <li> <a href="http://hgdownload-sd.sdsc.edu" target="_blank">http://hgdownload-sd.sdsc.edu</a></li> </ul> <p> <strong>The background</strong></p> <p> Typical TCP-based protocols like http, ftp and rsync have a problem in that the further away the download source is from you, the slower the speed becomes. Protocols like UDT/UDR allow for many UDP packets to be sent in batch, thus allowing for much higher transmit speeds over long distances. UDR will be especially useful for users who are downloading from locations distant to California. <em>The US East Coast and the international community will likely see much higher download speeds by using UDR rather than rsync, http or ftp.</em></p> <p> <strong>Getting UDR & setting it up on your system</strong></p> <p> It should be noted that UDR is not written or managed by UCSC, it was written by the Laboratory for Advanced Computing at the University of Chicago. It has been tested to work under Linux, FreeBSD and Mac OSX, but may work under other UNIX variants. The source code can be obtained here, through GitHub: <a href="https://github.com/LabAdvComp/UDR" target="_blank">https://github.com/LabAdvComp/UDR</a></p> <p> If you need help building the UDR binaries or have questions about how UDR functions, please read the documentation on the GitHub page, and if necessary, contact the UDR authors via the GitHub page. We recommend reading the documentation on the UDR GitHub page to better understand how UDR works. UDR is written in C++. UDR is Open Source and is released under the Apache 2.0 License. You must first have rsync installed on your system.</p> <p> For your convenience, we are offering a binary distribution of UDR for Red Hat Enterprise Linux 6.x and 7.x (or variants such as CentOS 6/7 or Scientific Linux 6/7). You'll find the rpm packages -here: <a href="http://hgdownload.soe.ucsc.edu/admin/udr" -target="_blank">http://hgdownload.soe.ucsc.edu/admin/udr</a>.</p> +here: <a href="http://hgdownload.gi.ucsc.edu/admin/udr" +target="_blank">http://hgdownload.gi.ucsc.edu/admin/udr</a>.</p> <p> For RHEL 6 we have 32-bit and 64-bit packages, but for RHEL 7 we have dropped the 32-bit and offer onlya 64-bit package. Those who need a 32-bit package for RHEL 7 can download the source and compile it locally.</p> <p> <strong>Example of using UDR to download ENCODE data from the UCSC Genome Browser Download Server</strong></p> <p> Once you have a working UDR binary, either by building from source or by installing the rpm (if you are using RHEL 6.x or other variant), you can download files from either of our download servers in a fashion very similar to rsync. For example, using rsync, you may want to download all of the ENCODE information for the mm9 database using the command:</p> -<pre><code>$ rsync -avP rsync://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/ /my/local/mm9/</code></pre> +<pre><code>$ rsync -avP rsync://hgdownload.gi.ucsc.edu/goldenPath/mm9/encodeDCC/ /my/local/mm9/</code></pre> <p> Using UDR is very similar. The UDR syntax for downloading the same data would be:</p> -<pre><code>$ udr rsync -avP hgdownload.soe.ucsc.edu::goldenPath/mm9/encodeDCC/ /my/local/mm9/</code></pre> +<pre><code>$ udr rsync -avP hgdownload.gi.ucsc.edu::goldenPath/mm9/encodeDCC/ /my/local/mm9/</code></pre> <p> If you installed the rpm, use the 'man udr' command for more information via the man page; if you installed from source please refer to the UDR GitHub page for more details on the capabilities of UDR and how to use it.</p> <p> <strong>Firewall Considerations</strong></p> <p> UDR establishes connections on TCP/9000, then transmits the data stream over UDP/9000-9100. Your institution may need to modify its firewall rules to allow inbound and outbound ports TCP/9000 and UDP/9000-9100 from either of the two download machines.</p> <p> If you decide to install and use UDR, we hope that you experience greatly increased download speeds. If you have difficulties installing UDR on your system, please contact the Laboratory for Advanced Computing through their github page: <a href="https://github.com/LabAdvComp/UDR" target="_blank">https://github.com/LabAdvComp/UDR</a>.</p> @@ -14178,32 +14178,32 @@ Flagged SNPs (142): uniquely mapped variants, excluding Common SNPs, that have been flagged by dbSNP as "clinically associated"</li> <li> Mult. SNPs (142): variants that have been mapped to more than one genomic location</li> </ul> <p> By default, only the Common SNPs (142) are visible; other tracks must be made visible using the track controls. You will find the other SNPs (142) tracks on both of GRCh37/hg19 and GRCh38/hg38 browsers in the Variation group.</p> <p> The tracks were produced at UCSC by Angie Hinrichs and Jonathan Casper. We'd like to thank the dbSNP group at NCBI for providing access to these data.</p> <p> As part of this release, we are also retiring the older dbSNP Build 135 and 137 data from display on the GRCh37/hg19 human assembly. Those tracks will still be available for viewing on our -<a href="http://genome-preview.soe.ucsc.edu" target="_blank">preview server</a>, and the associated -masked FASTA files will continue to be available on our <a href="http://hgdownload.soe.ucsc.edu" +<a href="http://genome-preview.gi.ucsc.edu" target="_blank">preview server</a>, and the associated +masked FASTA files will continue to be available on our <a href="http://hgdownload.gi.ucsc.edu" target="_blank">download server</a>. </p> <a name="020215"></a> <h2>Feb. 2, 2015 Host a Genome Browser workshop</h2> <p> New timeslots are now available to host a Genome Browser workshop at your institution. Thanks to the funding support of NHGRI, we offer hands-on Genome Browser training onsite at your institution, tailored to your audience's level of expertise.</p> <p> For more information or to submit a request to host a workshop, please visit <a href="http://bit.ly/ucscTraining" target="_blank">our sign-up page</a>.</p> <a name="012315"></a> <h2>Jan. 23, 2015 Genome Browser YouTube channel</h2> <p> @@ -14249,51 +14249,51 @@ PeptideAtlas team at the Institute for Systems Biology, Seattle for providing this data.</p> <!-- ============= 2014 archived news ============= --> <a name="2014"></a> <a name="121914"></a> <h2>Dec. 19, 2014 New cow (bosTau8) assembly now available in the Genome Browser</h2> <p> We are pleased to announce the release of a Genome Browser for the June 2014 assembly of cow, <i>Bos taurus</i> (Bos_taurus_UMD 3.1.1, UCSC version bosTau8). This updated cow assembly was provided by the <a href="http://www.cbcb.umd.edu/" target="_blank">UMD Center for Bioinformatics and Computational Biology</a> (CBCB). This assembly is an update to the previous UMD 3.1 (bosTau6) assembly. UMD 3.1 contained 138 unlocalized contigs that were found to be contaminants. These have been suppressed in UMD 3.1.1.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/bosTau8/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#cow">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/bosTau8/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#cow">Downloads</a> page. These data have <a href="/goldenPath/credits.html#cow_credits">specific conditions for use</a>. The cow browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="/goldenPath/credits.html#cow_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="121214"></a> <h2>Dec. 12, 2014 New <em>D. melanogaster</em> (dm6) assembly now available</h2> <p> We are pleased to announce the release of a Genome Browser for the August 2014 assembly of <em>Drosophila melanogaster</em> (BDGP Release 6, UCSC version dm6). This updated <em>D. melanogaster</em> assembly was provided by the <a href="http://www.fruitfly.org/" target="_blank">Berkeley Drosophila Genome Project</a> (BDGP). Please see <a href="http://flybase.org/static_pages/feature/previous/articles/2014_07/FB2014_04.html" target="_blank">this announcement</a> on the FlyBase website for more details about this updated <em>D. melanogaster</em> assembly.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/dm6/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#fruitfly">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/dm6/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#fruitfly">Downloads</a> page. These data have <a href="/goldenPath/credits.html#dm_credits">specific conditions for use</a>. The <i>D. melanogaster</i> (dm6) browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="/goldenPath/credits.html#dm_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="102914"></a> <h2>Oct. 9, 2014 Genome Browser in a Box (GBiB)</h2> <p> Sometimes you just want to keep your genomics data to yourself. Have you ever hesitated when uploading your data set into the UCSC Genome Browser? If so, you'll be happy to know that we have created a stand-alone personal version: Genome Browser in a Box (GBiB). If you have sensitive genomics data that you would like to view securely on your own laptop in the context of the UCSC Genome Browser, GBiB is for you.</p> <p> @@ -14374,32 +14374,32 @@ <a href="https://www.ncbi.nlm.nih.gov/nuccore/KM034562" target="_blank">KM034562</a>) submitted by the Broad Institute. We have worked closely with the Pardis Sabeti lab at the Broad Institute and other Ebola experts throughout the world to incorporate annotations that will be useful to those studying Ebola. Annotation tracks included in this initial release include genes from <a href="https://www.ncbi.nlm.nih.gov/" target="_blank">NCBI</a>, B- and T-cell epitopes from the <a href="http://www.iedb.org/" target="_blank">IEDB</a>, structural annotations from <a href="http://www.uniprot.org/" target="_blank">UniProt</a> and a wealth of SNP data from the <a href="https://www.ncbi.nlm.nih.gov/pubmed/25214632" target="_blank">2014 publication</a> by the Sabeti lab. This initial release also contains a 160-way alignment comprising 158 Ebola virus sequences from various African outbreaks and 2 Marburg virus sequences. You can find links to the Ebola virus Genome Browser and more information on the Ebola virus itself on our <a href="../ebolaPortal/">Ebola Portal</a> page.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/eboVir3/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#ebola_virus">Downloads</a> page. The Ebola +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/eboVir3/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#ebola_virus">Downloads</a> page. The Ebola virus (eboVir3) browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="credits.html#ebola_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release and conditions for use of these data.</p> <a name="092314"></a> <h2>Sep. 23, 2014 Ensembl Regulatory Build now available in the Genome Browser</h2> <p> We are pleased to announce that data from the <a href="http://www.ensembl.org/info/genome/funcgen/regulatory_build.html" target="_blank">Ensembl Regulatory Build</a> is now available in the UCSC Genome Browser as a public track hub for both hg19 and hg38. This track hub contains promoters and their flanking regions, enhancers, and many other regulatory features predicted across a number of cell lines using annotated segmentation states. Click <a href="/cgi-bin/hgTracks?db=hg19&position=chr21%3A33031597-33041570&hubUrl=http://ngs.sanger.ac.uk/production/ensembl/regulation/hub.txt">here</a> to view this hub on the hg19 assembly, or click @@ -14446,65 +14446,65 @@ <a name="073014"></a> <h2>Jul. 30, 2014 New rat (rn6) assembly now available</h2> <p> We are excited to announce the release of a Genome Browser for the July 2014 assembly of rat, <em>Rattus norvegicus</em> (RGSC Rnor_6.0, UCSC version rn6)! This assembly is provided by the Rat Genome Sequencing Consortium, which is comprised of eight research organizations across the United States and Canada and led by the <a href="https://www.hgsc.bcm.edu/" target="_blank">Baylor College of Medicine</a>. The new RGSC Rnor_6.0 assembly contains a new, partially assembled Y chromosome as well as improvements to other regions of the genome. You can find more information on the RGSC's efforts to sequence rat genome on the Baylor College of Medicine's <a href="https://www.hgsc.bcm.edu/other-mammals/rat-genome-project" target="_blank">project page</a>.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/rn6/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#rat">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/rn6/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#rat">Downloads</a> page. These data have <a href="../goldenPath/credits.html#rat_use">specific conditions for use</a>. The rat (rn6) browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="../goldenPath/credits.html#rat_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release. </p> <a name="071514b"></a> <p> <h2>Jul. 15, 2014 New shrew (sorAra2) assembly available in the Genome Browser</h2> <p> We are pleased to announce the release of a Genome Browser for the August 2008 assembly of shrew, <em>Sorex araneus</em> (Broad SorAra2.0, UCSC version sorAra2). The whole genome shotgun assembly was provided by <a href="http://www.broadinstitute.org/" target="_blank">The Broad Institute</a>. There are 12,845 scaffolds with a total size of 2,423,158,183 bases.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/sorAra2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#shrew">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/sorAra2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#shrew">Downloads</a> page. These data have <a href="/goldenPath/credits.html#shrew_credits">specific conditions for use</a>. The shrew (sorAra2) browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="/goldenPath/credits.html#shrew_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="071514a"></a> <h2>Jul. 15 2014 New pika (ochPri3) assembly released in the Genome Browser</h2> <p> We are pleased to announce the release of a Genome Browser for the May 2012 assembly of pika, <em>Ochotona princeps</em> (Broad OchPri3.0, UCSC version ochPri3). The whole genome shotgun assembly was provided by <a href="http://www.broadinstitute.org/" target="_blank">The Broad Institute</a>. There are 10,420 scaffolds with a total size of 2,229,835,716 bases.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/ochPri3/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#pika">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/ochPri3/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#pika">Downloads</a> page. These data have <a href="/goldenPath/credits.html#pika_credits">specific conditions for use</a>. The pika (ochPri3) browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="/goldenPath/credits.html#pika_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="061914"></a> <h2>Jun. 19, 2014 Conservation track released for rat</h2> <p> We are pleased to announce the release of a new Conservation track based on the rat (RGSC 5.0/rn5) assembly. This track shows multiple alignments of 13 vertebrate species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package for all species. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track. For more details, visit the <a href="../cgi-bin/hgTrackUi?db=rn5&g=cons13way"> track description page</a>.</p> @@ -14590,84 +14590,84 @@ >UCSC Genes track description page</a>.</p> <p> Many thanks to Brian Raney, Jim Kent, and Luvina Guruvadoo for their work on this track.</p> <a name="050914"></a> <h2>May 9, 2014 Three new assemblies now available in the Genome Browser</h2> <p> A Genome Browser is now available for the Chinese hamster (<em>Cricetulus griseus</em>) assembly released July 2013 by the <a href="http://www.genomics.cn/en/index" target="_blank">Beijing Genomics Institution-Shenzhen</a> (BGI version C_griseus_v1.0, UCSC version criGri1). For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/40911" target="_blank">C_griseus_v1.0</a>. There are 52,711 scaffolds with a total size of 2,360,146,428 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/criGri1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#chinese_hamster">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/criGri1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#chinese_hamster">Downloads</a> page. Please observe the <a href="credits.html#chinese_hamster_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators woldwide. See the <a href="credits.html#chinese_hamster_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <hr> <p> A Genome Browser is now available for the hedgehog (<em>Erinaceus europaeus</em>) assembly released May 2012 by the <a href="http://www.broadinstitute.org/" target="_blank">Broad Institute</a> (Broad version EriEur2.0, UCSC version eriEur2). For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/426148" target="_blank">EriEur2.0</a>. There are 5,802 scaffolds with a total size of 2,715,720,925 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/eriEur2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#hedgehog">Downloads</a> page. Please observe +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/eriEur2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#hedgehog">Downloads</a> page. Please observe the <a href="credits.html#hedgehog_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators woldwide. See the <a href="credits.html#hedgehog_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <hr> <p> A Genome Browser is now available for the zebra finch (<em>Taeniopygia guttata</em>) assembly released February 2013 by <a href="http://genome.wustl.edu/genomes/detail/taeniopygia-guttata/" target="_blank">The Genome Institute at Washington University</a> (WUSTL version Taeniopygia_guttata-3.2.4, UCSC version taeGut2). For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/524908" target="_blank">Taeniopygia_guttata-3.2.4</a>. There are 37,096 scaffolds with a total size of 1,232,135,591 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/taeGut2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#zebra_finch">Downloads</a> page. Please +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/taeGut2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#zebra_finch">Downloads</a> page. Please observe the <a href="credits.html#zebra_finch_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators woldwide. See the <a href="credits.html#zebra_finch_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="050814"></a> <h2>May 8, 2014 New elephant shark (calMil1) assembly now available</h2> <p> A Genome Browser is now available for the elephant shark (<em>Callorhinchus milii</em>) assembly released December 2013 by the <a href="http://www.imcb.a-star.edu.sg/" target="_blank">Singapore Institute of Molecular and Cell Biology</a> (IMCB version Callorhinchus_milii-6.1.3, UCSC version calMil1). For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/85971" target="_blank"> Callorhinchus_milii-6.1.3</a>. There are 21,204 scaffolds with a total size of 974,498,586 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/calMil1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#elephant_shark">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/calMil1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#elephant_shark">Downloads</a> page. Please observe the <a href="credits.html#elephant_shark_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators woldwide. See the <a href="credits.html#elephant_shark_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="050614"></a> <h2>May 6, 2014 Introducing the new stacked overlay for multi-wiggle tracks</h2> <p> We are excited to announce the release of the new stacked overlay method for multi-wiggle tracks. This new stacked overlay method displays each graph stacked on top of each other.</p> <p> <img src="../images/stackedMultiWig_screenshot.png" alt="Stacked screenshot" width="819" height="313"></p> <p> Navigate to the track settings for @@ -14724,32 +14724,32 @@ found in the Analysis Working Group Hub, but are now hosted natively in the Browser with enhanced filtering capability where desired segmented states can be selected using the Filter by Segment Type' control on the track configuration page.</p> <a name="041514"></a> <h2>Apr. 15, 2014 New minke whale (balAcu1) assembly now available</h2> <p> A Genome Browser is now available for the minke whale (Balaenoptera acutorostrata scammoni) assembly released October 2013 by the <a href="http://eng.kiost.ac/kordi_eng/main/" target="_BLANK"> Korea Ocean Research & Development Institute</a> (KORDI version BalAcu1.0, UCSC version balAcu1). For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/78761" target="_blank">BalAcu1.0</a>. There are 10,776 scaffolds with a total size of 2,431,687,698 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/balAcu1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#minke_whale">Downloads</a> page. Please +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/balAcu1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#minke_whale">Downloads</a> page. Please observe the <a href="credits.html#minke_whale_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#minke_whale_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="041114"></a> <h2>Apr. 11, 2014 New UCSC Genes track released for GRCm38/mm10</h2> <p> We're happy to announce the release of an updated UCSC Genes track for the GRCm38/mm10 mouse Genome Browser. The new release has 61,642 total transcripts, compared with 59,121 in the previous version. The total number of canonical genes has increased from 31,469 to 32,408. Comparing the new gene set with the previous version:</p> <ul> <li> 54,714 transcripts did not change between versions.</li> @@ -14818,42 +14818,42 @@ <a href="http://mitomap.org/MITOMAP" target="_blank">MITOMAP</a> with GenBank accession number J01415.2 and RefSeq accession number NC_012920.1. This differs from the chrM sequence (RefSeq accession number NC_001907) used by the previous hg19 Genome Browser, which was not updated when the GRCh37 assembly later transitioned to the new version.</li> <li> <strong>Sequence updates</strong> - Several erroneous bases and misassembled regions in GRCh37 have been corrected in the GRCh38 assembly, and more than 100 gaps have been filled or reduced. Much of the data used to improve the reference sequence was obtained from other genome sequencing and analysis projects, such as the <a href="http://www.1000genomes.org/" target="_blank">1000 Genomes Project</a>.</li> <li> <strong>Analysis set</strong> - The GRCh38 assembly offers an "analysis set" that was created to accommodate next generation sequencing read alignment pipelines. Several GRCh38 regions have been eliminated from this set to improve read mapping. The analysis set may be downloaded from the Genome Browser - <a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/" + <a href="http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/" target="_blank">downloads page</a>.</li> </ul> <p> For more information about the files included in the GRCh38 GenBank submission, see the <a href="ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/README" target="_blank">GRCh38 README</a>. The GRCh38 GenBank record provides a detailed array of <a href="https://www.ncbi.nlm.nih.gov/assembly/883148/#/st_Primary-Assembly" target="_blank">statistics about this assembly</a>. Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg38/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#human">Downloads</a> page. The annotation +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg38/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#human">Downloads</a> page. The annotation tracks for this browser were generated by UCSC and collaborators worldwide.</p> <p> <strong>Much more to come!</strong> This initial release of the hg38 Genome Browser provides a rudimentary set of annotations. Many of our annotations rely on data sets from external contributors (such as our popular SNPs tracks) or require massive computational effort (our comparative genomics tracks). In the upcoming months/years, we will release many more annotation tracks as they become available. To stay abreast of new datasets, join our <a href="http://groups.google.com/a/soe.ucsc.edu/group/genome-announce?hl=en" target="_blank">genome-announce</a> mailing list or follow us on <a href="http://www.twitter.com/GenomeBrowser" target="_blank">twitter</a>.</p> <p> We'd like to thank our GRC and NCBI collaborators who worked closely with us in producing the hg38 browser. Their quick responses and helpful feedback were a key factor in expediting this release. The production of the hg38 Genome Browser was a team effort, but in particular we'd like to acknowledge the engineering efforts of Hiram @@ -15019,81 +15019,81 @@ site for the new and improved site. For more background on DGV's changes, please see DGV's <a href="http://dgv.tcag.ca/dgv/app/news" target="_blank">June 2013 newsletter</a>.</p> <a name="092613"></a> <h2>Sep. 26, 2013 New American alligator (allMis1) assembly now available</h2> <p> A Genome Browser is now available for the American alligator (<em>Alligator mississippiensis</em>) assembly released August 2012 by the International Crocodilian Genomes Working Group (version allMis0.2, UCSC version allMis1). Please note the <a href="https://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AKHW01" target="_blank">assembly construction details</a>. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/406428/" target="_blank">allMis0.2</a>. There are 14,645 scaffolds with a total size of 2,174,259,888 bases.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/allMis1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#american_alligator">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/allMis1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#american_alligator">Downloads</a> page. Please observe the <a href="credits.html#american_alligator_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#american_alligator_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release. </p> <a name="091113"></a> <h2>Sep. 11, 2013 New alpaca (vicPac2) assembly released in the Genome Browser</h2> <p> We are pleased to announce the release of a Genome Browser for the March 2013 assembly of alpaca, <em>Vicugna pacos</em> (Broad Vicugna_pacos-2.0.1, UCSC version vicPac2). The whole genome shotgun assembly was provided by <a href="http://www.broadinstitute.org/" target="_blank">The Broad Institute</a>. There are 276,725 scaffolds with a total size of 2,172,191,320 bases.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/vicPac2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#alpaca">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/vicPac2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#alpaca">Downloads</a> page. These data have <a href="/goldenPath/credits.html#alpaca_credits">specific conditions for use</a>. The alpaca browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="/goldenPath/credits.html#alpaca_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release. </p> <a name="090413b"></a> <h2>Sep. 4, 2013 New tenrec (echTel2) assembly added to the Genome Browser</h2> <p> We are pleased to announce the release of a Genome Browser for the Nov. 2012 assembly of tenrec, <em>Echinops telfairi</em> (Broad EchTel2.0, UCSC version echTel2). The whole genome shotgun assembly was provided by <a href="http://www.broadinstitute.org/" target="_blank">The Broad Institute</a>. There are 8,402 scaffolds with a total size of 2,947,024,286 bases.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/echTel2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#tenrec">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/echTel2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#tenrec">Downloads</a> page. These data have <a href="/goldenPath/credits.html#tenrec_credits">specific conditions for use</a>. The tenrec browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="/goldenPath/credits.html#tenrec_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="090413a"></a> <h2>Sep. 4, 2013 New sheep (oviAri3) assembly now available</h2> <p> We are pleased to announce the release of a Genome Browser for the August 2012 assembly of sheep, <em>Ovis aries</em> (ISGC Oar_v3.1, UCSC version oviAri3). The whole genome shotgun assembly was provided by the <a href="http://www.sheephapmap.org" target="_blank">International Sheep Genomics Consortium</a>. There are 5,698 scaffolds with a total size of 2,619,054,388 bases.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/oviAri3/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#sheep">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/oviAri3/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#sheep">Downloads</a> page. These data have <a href="/goldenPath/credits.html#sheep_credits">specific conditions for use</a>. The sheep browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="/goldenPath/credits.html#sheep_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="082213"></a> <h2>Aug. 22, 2013 Three new human variation tracks released</h2> <p> We are pleased to announce the release of three tracks that describe human genetic variation. They are based on the <a href="http://lovd.nl/2.0/index_list.php" target="_blank">Leiden Open Variation Database (LOVD)</a>, the <a href="http://www.hgmd.cf.ac.uk/ac/index.php" target="_blank">Human Gene Mutation Database Public (HGMD)</a>, and amino acid mutations in the <a href="http://www.uniprot.org/" target="_blank">UniProt database</a>. The majority of the data were collected from publications by curators in the three databases.</p> <p> @@ -15253,50 +15253,50 @@ our mailing lists. You may reach the suggestion box from the <a href="../contacts.html" target="_blank">Contact Us</a> page or by <a href="../cgi-bin/hgUserSuggestion" target="_blank">clicking here</a>. </p> <a name="061213"></a> <h2>Jun. 12, 2013 Ferret Genome Browser released</h2> <p> A Genome Browser is now available for the ferret (<em>Mustela putorius furo</em>) assembly released by the Ferret Genome Sequencing Consortium April 2011 (version MusPutFur1.0, UCSC version musFur1). Please note the <a href="https://www.ncbi.nlm.nih.gov/Traces/wgs/?val=AEYP01" target="_blank">assembly construction details</a>. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/286418/" target="_blank">MusPutFur1.0</a>.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/musFur1/" target="_blank">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#ferret" target="_blank">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/musFur1/" target="_blank">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#ferret" target="_blank">Downloads</a> page. Please observe the <a href="credits.html#ferret_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#ferret_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="052213"></a> <h2>May 22, 2013 Gibbon Genome Browser released</h2> <p> A Genome Browser is now available for the Gibbon (<em>Nomascus leucogenys</em>) assembly released by the Gibbon Genome Sequencing Consortium Oct. 2012 (version Nleu_3.0, UCSC version nomLeu3). Please note the <a href="https://www.ncbi.nlm.nih.gov/Traces/wgs/?val=ADFV01" target="_blank">assembly construction details</a>. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/506498/" target="_blank">Nleu_3.0</a>.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/nomLeu3/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#gibbon">Downloads</a> page. Please observe +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/nomLeu3/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#gibbon">Downloads</a> page. Please observe the <a href="credits.html#gibbon_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#gibbon_credits">Credits</a> page for a detailed the organizations and individuals who contributed to this release.</p> <a name="040913"></a> <h2>Apr. 9, 2013 The UCSC Cancer Genomics Browser has a new look</h2> <p> The UCSC Cancer Genomics group has recently remodeled the interface of the <a href="https://genome-cancer.ucsc.edu/" target="blank">Cancer Genomics Browser</a> to make it easier to navigate and more intuitive to display, investigate, and analyze cancer genomics data and associated clinical information. This tool provides access to many types of information—biological pathways, collections of genes, genomic and clinical information—that can be used to sort, aggregate, and perform statistical tests on a group of samples. The Cancer Browser currently displays 473 datasets of 25 cancers from @@ -15368,67 +15368,67 @@ Genome Browser with these data. We'd also like to acknowledge the hard work of the UCSC Genome Browser staff who pulled together the annotations and information for these tracks: Angie Hinrichs and Pauline Fujita.</p> <a name="012513"></a> <h2>Jan. 25, 2013 Southern white rhinoceros Genome Browser released</h2> <p> A Genome Browser is now available for the Southern White Rhinoceros (<em>Ceratotherium simum simum</em>) assembly released by the Broad Institute in May 2012 (Broad version cerSimSim1.0, UCSC version cerSim1). This genome was sequenced and assembled at the Broad Institute using samples provided by Dr. Oliver Ryder at the San Diego Zoo Institute for Conservation Research. For more information and statistics about this assembly, see the NCBI assembly record for <a href="https://www.ncbi.nlm.nih.gov/assembly/406328/" target="_blank">CerSimSim1.0</a>.</p> <p> Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/cerSim1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#white_rhinoceros">Downloads</a> page. Please +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/cerSim1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#white_rhinoceros">Downloads</a> page. Please observe the <a href="credits.html#white_rhinoceros_use">conditions for use</a> when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the <a href="credits.html#white_rhinoceros_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="012213"></a> <h2>Jan. 22, 2013 New baboon (papAnu2) assembly now available in the Genome Browser</h2> <p> We are pleased to announce the release of a Genome Browser for the March 2012 assembly of the olive baboon, <em>Papio anubis</em> (Baylor Panu_2.0, UCSC version papAnu2). The whole genome shotgun assembly was provided by <a href="https://www.hgsc.bcm.edu/content/baboon-genome-project" target="_blank">The Baylor College of Medicine Human Genome Sequencing Center</a>. There are 72,500 scaffolds with a total size of 2,948,380,710 bases.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/papAnu2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#baboon">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/papAnu2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#baboon">Downloads</a> page. These data have <a href="/goldenPath/credits.html#baboon_credits">specific conditions for use</a>. The baboon browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="/goldenPath/credits.html#baboon_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="011513"></a> <h2>Jan. 15, 2013 New lamprey (petMar2) assembly released in Genome Browser</h2> <p> We are pleased to announce the release of a Genome Browser for the Sep. 2010 assembly of the lamprey, <em>Petromyzon marinus</em> (WUGSC 7.0, UCSC version petMar2). The whole genome shotgun assembly was provided by <a href="http://genome.wustl.edu/genomes/detail/petromyzon-marinus/" target="_blank">The Genome Institute at Washington University</a>. There are 25,006 scaffolds with a total size of 885,550,958 bases.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/petMar2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#lamprey">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/petMar2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#lamprey">Downloads</a> page. These data have <a href="/goldenPath/credits.html#lamprey_credits">specific conditions for use</a>. The lamprey browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="/goldenPath/credits.html#lamprey_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <!-- ============= 2012 archived news ============= --> <a name="2012"></a> <a name="122012"></a> <h2>Dec. 20, 2012 28 new vertebrate assemblies</h2> <p> Over the past several weeks, we have released 28 new vertebrate assemblies on the public Genome Browser website, featuring 22 new species and 6 assembly updates. These assemblies were added to support the 60-species Conservation track on the latest mouse assembly (mm10/GRCm38). Several of these species were originally sequenced and assembled for the Mammalian Genome Project (Lindblad-Toh <em>et al</em>., <em>Nature</em> 2011)*.</p> @@ -15522,32 +15522,32 @@ <strong>Budgerigar</strong> (<em>Melopsittacus undulatus</em>) <strong>melUnd1</strong> – v6.3 (Sep. 2011) from WUSTL</li> <li> <strong>Coelacanth</strong> (<em>Latimeria chalumnae</em>) <strong>latCha1</strong> – LatCha1 (Aug. 2011) from the Broad Institute</li> <li> <strong>Nile tilapia</strong> (<em>Oreochromis niloticus</em>) <strong>oreNil2</strong> – OreNil1.1 (Jan. 2011) from the Broad Institute</li> </ul> <p> Our sincere thanks to the many organizations who contributed to the release of these datasets. We'd also like to acknowledge the Genome Browser staff who worked on this release: Hiram Clawson, Chin Li, Brian Raney, Brooke Rhead, Steve Heitner, Pauline Fujita, Luvina Guruvadoo, Greg Roe, and Donna Karolchik. Please see the Genome Browser <a href="credits.html">credits page</a> for complete acknowledgment information and data use restrictions. All datasets may be downloaded from our -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/">ftp server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html">downloads</a> page.</p> +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/">ftp server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html">downloads</a> page.</p> <p> We regret that we don't have the resources to support the many other genomics research communities who would like us to visualize their data in our browser. However, we can provide you with information for setting up your own browser or track hub to display your data, as well as links to other visualization resources on the web that are specific to your genome of interest. Feel free to contact our <a href="mailto:genome@soe.ucsc.edu">mail list</a> for more information.</p> <p> *Lindblad-Toh K <em>et al</em>. <a href="http://www.nature.com/nature/journal/v478/n7370/full/nature10530.html" target="_blank">A high-resolution map of human evolutionary constraint using 29 mammals</a>. <em>Nature</em>. 2011 Oct 12;478(7370):476-82.</p> <a name="120712"></a> <h2>Dec. 7, 2012 dbSNP 137 available for hg19</h2> <p> @@ -15643,32 +15643,32 @@ naturalist Charles Darwin's Galapagos finches. This species, which has been the subject of many evolutionary studies, is one of a group of birds that evolved over a few million years from a single ancestral species into multiple species whose beak sizes and shapes are specialized for using different food resources. The phenotypic diversity of these birds contributed to Darwin's theory of evolution. The significance of this genome assembly is described in the Aug. 16, 2012, <a href="https://cbse.soe.ucsc.edu/news/article/1939" target="_blank">press release</a> issued by the UCSC Center for Biomolecular Science and Engineering (CBSE).</p> <p> The initial Medium ground finch genome assembly (GeoFor_1.0, UCSC version geoFor1) is the product of a collaboration between the Genome 10K project and Beijing Genomics Institute (BGI) to sequence 100 vertebrate species, and is the first to be released in the UCSC Genome Browser. For more information about the <em>G. fortis</em> genome, see the <a href="https://www.ncbi.nlm.nih.gov/genome/13302" target="_blank">NCBI website</a>.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/geoFor1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#mediumgroundfinch">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/geoFor1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#mediumgroundfinch">Downloads</a> page. The browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="credits.html#mediumgroundfinch_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release. We'd like to thank BGI for contributing the data for this assembly and acknowledge the UCSC staff members who released this browser: Hiram Clawson and Greg Roe.</p> <a name="081412"></a> <h2>Aug. 14, 2012 Changes to our website</h2> <p> We are pleased to announce a few changes to the look and feel of the Genome Browser website. In addition to a new font throughout the site, the first thing you might notice is a new menu bar across the top of many of the pages. We have reorganized the navigation on our web applications with you in mind; we hope you find it more intuitive! </p> <p> Additionally, we greatly simplified the search mechanism by collapsing all search methods into a @@ -15684,32 +15684,32 @@ <a name="071612"></a> <h2>Jul. 16, 2012 Tasmanian devil assembly now available in Genome Browser</h2> <p> We are pleased to announce the release of a Genome Browser for the Feb. 2011 Tasmanian devil assembly, <em>Sarcophilus harrisii</em> (WTSI version Devil_refv7.0, UCSC version sarHar1). The Tasmanian devil, which is native to the island of Tasmania, is at risk of extinction due to a transmissible facial cancer. The devil population in Tasmania has declined by more than 80% since the first time the disease was observed 14 years ago. This draft assembly, created by the <a href="http://www.sanger.ac.uk/" target="_blank">Wellcome Trust Sanger Institute</a>, was sequenced using Illumina reads. This completed genome is the first step towards finding genetic mutations in the transmissible cancer, which will help researchers understand the disease and its spread.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/sarHar1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#tasmanian_devil">Downloads</a> page. The +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/sarHar1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#tasmanian_devil">Downloads</a> page. The Tasmanian devil browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="credits.html#tasmanian_devil_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="070612"></a> <h2>Jul. 6, 2012 Retirement of hgText CGI</h2> <p> We are announcing the imminent retirement of the hgText CGI. hgText was the original version of the Table Browser, and was replaced by the new CGI, hgTables, in <a href="#100104">2004</a>. A very small number of our users still access the database using the old hgText CGI. We plan to remove hgText from our site on Jul. 24, 2012, after which all users must use hgTables.</p> <a name="061912"></a> <h2>Jun. 19, 2012 Many new assemblies available in the browser</h2> <p> @@ -15786,71 +15786,71 @@ <li> <strong>Turkey</strong> (<em>Meleagris gallopavo</em>) <strong>melGal1</strong> – Turkey_2.01 (Dec. 2009) from the Turkey Genome Consortium</li> <li> <strong>Western clawed frog</strong> (<em>X. tropicalis</em>) <strong>xenTro3</strong> – v4.2 (Nov. 2009) from the DOE Joint Genome Institute</li> <li> <strong><em>C. elegans</em></strong> <strong>ce10</strong> – WS220 (Oct. 2010) from WormBase</li> <li> <strong><em>S. cerevisiae</em></strong> <strong>sacCer3</strong> – SacCer_Apr2011 (Apr. 2011) from the Saccharomyces Genome Database</li> </ul> <p> Bulk downloads of the sequence and annotation data for these assemblies are available via the Genome -Browser <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/" target="_blank">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html" target="_blank">Downloads</a> page. Be sure +Browser <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/" target="_blank">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html" target="_blank">Downloads</a> page. Be sure to check the <a href="credits.html">credits</a> page for data use restrictions and acknowledgments.</p> <p> Many thanks to the sequencing and assembly groups, as well as NCBI's GenBank, for making these genomes available for public use. We'd also like to acknowledge Hiram Clawson, Chin Li, and our hard-working QA team for putting together these browsers.</p> <a name="051512b"></a> <h2>May 15, 2012 New Fugu (fr3) assembly now available in the Genome Browser</h2> <p> We are pleased to announce the release of a Genome Browser for the October 2011 assembly of the Fugu, <em>Takifugu rubripes</em> (JGI v5.0, UCSC version fr3). The whole genome shotgun assembly was provided by the <a target="_blank" href="http://www.fugu-sg.org/">International Fugu Genome Sequencing Consortium</a> led by JGI and the <a target="_blank" href="http://www.imcb.a-star.edu.sg/">Singapore Institute of Molecular and Cell Biology</a> (IMCB).</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/fr3/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#fugu">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/fr3/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#fugu">Downloads</a> page. These data have <a href="http://genome.jgi-psf.org/Takru4/Takru4.download.html" target="_blank">specific conditions for use</a>. The Fugu (fr3) browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="credits.html#fugu_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="051512a"></a> <h2>May 15, 2012 Naked mole-rat assembly now available in Genome Browser</h2> <p> We are pleased to announce the release of a Genome Browser for the July 2011 Naked mole-rat, <em>Heterocephalus glaber</em> (BGI version HetGla1.0, UCSC version hetGla1). This draft assembly, produced by the <a href="http://www.genomics.cn/en/index" target="_blank">Beijing Genomics Institute</a>, has been sequenced using Illumina reads with a sequencing depth of >20x. There are 39,266 scaffolds with a total size of 2,643,961,837 bases. The N50 size of the scaffolds is 1,603,177 bases with 502 scaffolds larger, and 38,764 scaffolds smaller. The mitochondrial sequence is also available as the virtual chromosome "chrM".</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/hetGla1/" target="_blank">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#naked_mole-rat" target="_blank">Downloads</a> +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/hetGla1/" target="_blank">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#naked_mole-rat" target="_blank">Downloads</a> page. These data have <a href="credits.html#naked_mole-rat_use">specific conditions for use</a>. The naked mole-rat browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="credits.html#naked_mole-rat_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="050812"></a> <h2>May 8, 2012 OpenHelix to conduct free Genome Browser webinars in May</h2> <p> <a href="http://www.openhelix.com" target="_blank">OpenHelix</a> is conducting two free webinars on the UCSC Genome Browser:</p> <ul> <li> UCSC Genome Browser: An Introduction (Thursday, May 17, 1pm EDT) -- designed for new users of the UCSC Genome Browser and those who want to improve their skills at basic navigation and display.</li> @@ -15917,32 +15917,32 @@ <a href="https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/contact.shtml" target="_blank">like your input</a>.</p> <a name="030712"></a> <h2>Mar. 7, 2012 New mouse browser available</h2> <p> We have released the latest Genome Browser for the Dec. 2011 mouse genome assembly produced by the <a href="https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/" target="_blank">Mouse Genome Reference Consortium</a> (Genome Reference Consortium GRCm38, UCSC version mm10). This version, which includes approximately 2.6 Gb of sequence, is considered to be "essentially complete". The assembly includes chromosomes 1-19, X, Y, M (mitochondrial DNA) and chr*_random (unlocalized) and chrUn_* (unplaced clone contigs). Note that the UCSC mm10 database contains only the reference strain C57BL/6J.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/mm10/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#mouse">Downloads</a> page. The mouse browser +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/mm10/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#mouse">Downloads</a> page. The mouse browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="credits.html#mouse_credits" target="_blank">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="022912"></a> <h2>Feb. 29, 2012 RGD Genes available for rn4</h2> <p> We are pleased to announce the release of RGD Genes for rat (Baylor 3.4/rn4). This track shows protein-coding gene annotations curated by <a href="http://rgd.mcw.edu/" target="_blank">RGD</a>. This track replaces UCSC Known Genes as the main gene track for this assembly.</p> <p> More details about this track can be found on the <a href="../cgi-bin/hgTrackUi?db=rn4&g=rgdGene2" target="_blank">RGD Genes track description page</a>.</p> <p> We'd like to thank RGD for providing the base annotations for this track. The RGD Genes track was @@ -16029,32 +16029,32 @@ Many thanks to Melissa Cline, Jim Kent, Brian Raney, Mark Diekhans, and Brooke Rhead for their work on this track.</p> <a name="230112"></a> <h2>Jan. 23, 2012 Wallaby browser available</h2> <p> We have released a Genome Browser for the September 2009 genome assembly of the Tammar wallaby, <em>Macropus eugenii</em> (TWGS version Meug_1.1, UCSC version macEug2). This assembly, which has been sequenced to 2X coverage, was produced by the Tammar Wallaby Genome Sequencing Consortium, a collaboration between the Baylor College of Medicine <a href="http://www.hgsc.bcm.tmc.edu/project-species-m-Wallaby.hgsc" target="_blank">Human Genome Sequencing Center</a> and the <a href="http://www.agrf.org.au/" target="_blank">Australian Genome Research Facility</a>.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/macEug2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#wallaby">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/macEug2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#wallaby">Downloads</a> page. These data have <a href="credits.html#wallaby_use">specific conditions for use</a>.</p> <p> We'd like to thank the Tammar Wallaby Genome Sequencing Consortium for providing this assembly. The wallaby browser and annotation tracks were produced by Chin Li and Luvina Guruvadoo. See the <a href="credits.html#wallaby_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="030112"></a> <h2>Jan. 3, 2012 Roadmap Epigenomics now available through data hub at Washington University</h2> <p> We are pleased to announce the release of the Roadmap Epigenomics data on the UCSC Genome Browser through our data hub utility. The Roadmap Epigenomics Project is part of The NIH Common Fund's <a href="https://commonfund.nih.gov/epigenomics/" target="_blank">Epigenomics Program</a>. It was launched with the goal of producing a public resource of human epigenomic data to catalyze @@ -16098,51 +16098,51 @@ (Nov. 2009, UCSC bosTau6) was produced by the <a href="http://www.cbcb.umd.edu/" target="_blank">UMD Center for Bioinformatics and Computational Biology</a> (CBCB) in College Park, MD.</p> <p> The UMD 3.1 assembly is based on reads downloaded from the NCBI Trace Archive, most of which were sequenced by the Baylor College of Medicine. UMD reports that they were able to apply several assembly improvement techniques to produce an assembly that is substantially more accurate and complete than previous alternative versions, as evaluated using independent metrics. Based on UMD statistics, this assembly provides more genome coverage, closes thousands of gaps, corrects many erroneous inversions, deletions, and translocations, and fixes thousands of single-nucleotide errors. For more information, see Zimin, AV <em>et al.</em>, <a href="http://genomebiology.com/2009/10/4/R42" target="_blank">A whole-genome assembly of the domestic cow, <em>Bos taurus</em></a>, <em>Genome Biol.</em> 2009;10(4). </p> <p> Downloads of the UMD bovine data and annotations may be obtained from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/bosTau6/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#cow">Downloads</a> page.</p> +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/bosTau6/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#cow">Downloads</a> page.</p> <p> We'd like to thank the UMD CBCB for providing this genome assembly. The UMD Cow Genome Browser and annotation tracks were produced by Hiram Clawson, Chin Li, Brooke Rhead, Greg Roe, Steve Heitner, and Donna Karolchik. See the <a href="credits.html#cow_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.<p> <a name="101011"></a> <h2>Oct. 10, 2011 Updated yeast browser released</h2> <p> We are happy to announce the release of an updated browser for the <em>Saccharomyces cerevisiae</em> yeast genome. The April 2011 sacCer3 assembly corresponds to the S288c assembly produced by the <a href="http://www.yeastgenome.org/" target="_blank">Saccharomyces Genome Database</a> (SGD) project. For more information on this genome, see the <a href="http://www.yeastgenome.org/cache/genomeSnapshot.html" target="_blank">SGD Genome Overview</a>.</p> <p> Downloads of the yeast data and annotations may be obtained from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/" target="_blank">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#yeast" target="_blank">Downloads</a> +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/sacCer3/" target="_blank">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#yeast" target="_blank">Downloads</a> page.</p> <p> We'd like to thank the SGD for providing this genome assembly. The <em>S. cerevisiae</em> Genome Browser and annotation tracks were produced by Hiram Clawson, Greg Roe, and Steve Heitner. See the <a href="credits.html#yeast_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="090811"></a> <h2>Sep. 8, 2011 New navigation and display features</h2> <p> We've added several new features to the Genome Browser that make it easier to quickly configure and navigate around in the browser's annotation tracks window.</p> <p> <strong>Automatic image resizing:</strong> The first time the annotation track window is displayed, or after the Genome Browser has been reset, the size of the track window is now set by default to @@ -16243,32 +16243,32 @@ weekly mirror of our internal development server for public access. Data and tools there are under construction, have not been quality reviewed, and are subject to change at any time. We provide this site for early access, with the warning that it is less available and stable than our public site. For high-quality reviewed annotations on our production server, visit our public website: <a href="../index.html">http://genome.ucsc.edu</a>.</p> <a name="060711"></a> <h2>Jun. 7, 2011 Updated lizard browser available</h2> <p> We have released a Genome Browser for the May 2010 genome assembly of the green anole lizard, <em>Anolis carolinensis</em> (Broad version AnoCar2.0, UCSC version anoCar2). This assembly, which has been sequenced to 7.1X coverage, was produced by the <a href="http://www.broad.mit.edu/" target="_blank">Broad Institute</a>, Cambridge, MA.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/anoCar2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#lizard">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/anoCar2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#lizard">Downloads</a> page. These data have <a href="credits.html#lizard_use">specific conditions for use</a>.</p> <p> We'd like to thank the Broad Institute for providing this assembly. The lizard Genome Browser and annotation tracks were produced by Hiram Clawson, Brian Raney, and Luvina Guruvadoo. See the <a href="credits.html#lizard_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="052611"></a> <h2>May 26, 2011 New release of UCSC Genes for mouse</h2> <p> We've released an updated set of UCSC Genes for the mm9 (NCBI Build 37) mouse browser. This version of the gene set was generated using the same computational pipeline as the previous mm9 UCSC Genes, but is based on more recent GenBank data.</p> <p> The new release has 55,419 total transcripts, compared with 49,409 in the previous version. The @@ -16439,62 +16439,62 @@ This assembly covers about 97 percent of the genome and is based on 6X sequence coverage. It comprises 192,898 contigs with an N50 length of 44 kb and 33,990 supercontigs with an N50 length of 8.4 Mb. Improvements introduced with the 2.1.3 assembly include the addition of over 300,000 finishing reads and the merging in of 640 finished BACS. Approximately 49,000 additional merges were made in this assembly as compared with the 2.1 assembly.</p> <p> The whole genome shotgun data were derived primarily from the donor Clint, a captive-born male chimpanzee from the Yerkes Primate Research Center in Atlanta, GA, USA. The sequence data were assembled and organized by the Washington University Genome Center. The underlying whole genome shotgun data were generated at the Washington University School of Medicine and the Broad Institute. For detailed information about the assembly process, see the sequencing and analysis discussion in the <a href="https://www.ncbi.nlm.nih.gov/nuccore/AACZ00000000" target="_blank">GenBank accession record</a>.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/panTro3/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#chimp">Downloads</a> page. The complete set +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/panTro3/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#chimp">Downloads</a> page. The complete set of sequence reads is available at the <a href="https://www.ncbi.nlm.nih.gov/Traces" target="_blank">NCBI trace archive</a>. These data have <a href="credits.html#chimp_use">specific conditions for use</a>.</p> <p> We'd like to thank the International Chimpanzee Sequencing and Analysis Consortium, Washington University at St. Louis School of Medicine Genome Sequencing Center, and the Broad Institute for providing this assembly. We'd also like to acknowledge the UCSC team who worked on this release: Hiram Clawson, Greg Roe, and Donna Karolchik. The chimpanzee browser annotation tracks were generated by UCSC and collaborators worldwide.</p> <a name="011911"></a> <h2>Jan. 19, 2011 Browser released for zebrafish Zv9 assembly</h2> <p> The most recent zebrafish assembly -- Zv9 (UCSC version danRer7, Jul. 2010) -- is now available in the UCSC Genome Browser. This assembly was produced by <a href="http://www.sanger.ac.uk/" target="_blank">The Wellcome Trust Sanger Institute</a>, UK.</p> <p> The Zv9 assembly comprises a sequence length of 1.4 Gb in 26 chromosomes and 1,107 scaffolds. This assembly is based on a clone path sorted with the high-density meiotic map SATMAP (Clark et al., in preparation). The data freeze was taken on Apr. 1, 2010. The remaining gaps were filled with sequence from WGS31, a combined Illumina and capillary assembly. The assembly integration process involved sequence alignemnts as well as cDNA, marker and BAC/Fosmid end sequence placements. The zebrafish mitochondrial sequence is also available in the Genome Browser as the virtual chromosome, chrM. For more details about the Zv9 assembly, see the Sanger Institute page for the <a href="http://www.sanger.ac.uk/Projects/D_rerio/Zv9_assembly_information.shtml" target="_blank"><em>Danio rerio</em> Sequencing Project</a>.</p> <p> The danRer7 sequence and annotation data can be downloaded from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/danRer7/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#zebrafish">downloads</a> page. Please review +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/danRer7/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#zebrafish">downloads</a> page. Please review the Sanger Institute <a href="http://www.sanger.ac.uk/legal/" target="_blank">guidelines</a> for using these data.</p> <p> We'd like to thank the Wellcome Trust Sanger Institute for providing this assembly. The UCSC zebrafish Genome Browser was produced by Hiram Clawson, Greg Roe, Mary Goldman, Brian Raney and Donna Karolchik. See the <a href="credits.html#zebrafish_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="011011"></a> <h2>Jan. 10, 2011 Introducing Genome Browser right-click navigation</h2> <p> Several of the common display and navigation operations offered on the Genome Browser tracks page may now be quickly accessed by right-clicking on a feature on the tracks image and selecting an option from the displayed menu. Depending on context, the right-click feature will let you change the track display mode, zoom in or out to the exact position coordinates of the feature, open the @@ -16605,32 +16605,32 @@ see the <a href="../cgi-bin/hgTrackUi?db=hg18&c=chr1&g=wgEncodeReg">track description</a> page.</p> <a name="081810"></a> <h2>Aug. 18, 2010 Cat Genome Browser available</h2> <p> We have released a Genome Browser for the latest assembly of Cat (<em>Felis catus</em>). The GTB V17E assembly (Dec. 2008, UCSC version felCat4) was produced by the NHGRI Genome Technology Branch and NIH Intramural Sequencing Center, Maryland; Agencourt Bioscience Corporation, Massachusetts; NCI Laboratory of Genomic Diversity, Maryland; and Hill's Pet Nutrition, Inc, Kansas. The mitochondrial genome was sequenced by NCI Laboratory of Genomic Diversity. For detailed sequencing and assembly information, see the NCBI Felis catus <a href="https://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=10703" target="_blank">assembly page</a>.</p> <p> Downloads of the Cat data and annotations may be obtained from the -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/felCat4/">UCSC FTP site</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#cat">Downloads</a> page. These data have been +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/felCat4/">UCSC FTP site</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#cat">Downloads</a> page. These data have been freely provided for use in the UCSC Genome Browser with specific conditions for use.</p> <p> Many thanks to NHGRI, Agencourt Bioscience Corporation, NCI and Hill's Pet Nutrition for providing these data. The felCat4 annotation tracks were generated by UCSC and its collaborators. We'd also like to acknowledge the UCSC Cat browser team: Chin Li, Antonio Coelho, Mary Goldman and Donna Karolchik. See the <a href="credits.html#cat_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="072310"></a> <h2>Jul. 23, 2010 BigBed/BigWig paper published</h2> <p> Last summer, we announced the release of new data formats for very large data sets: BigBed and BigWig. Read more about these data formats <a href="https://lists.soe.ucsc.edu/pipermail/genome-announce/2009-July/000165.html" target="_blank">here</a>. As a follow up, we are pleased to announce that we have published a paper @@ -16732,32 +16732,32 @@ Goldman.</p> <a name="060310"></a> <h2>Jun. 3, 2010 Updated marmoset browser available</h2> <p> We have released an updated marmoset (<em>Callithrix jacchus</em>) assembly, UCSC version calJac3, corresponding to the Mar. 2009 v3.2 assembly from the Genome Center at Washington University St. Louis School of Medicine (WUSTL).</p> <p> This draft of the marmoset genome has approximately 6X coverage. For statistics and details on the assembly process, see the WUSTL Callithrix jacchus <a href="http://genome.wustl.edu/genomes/detail/callithrix-jacchus/" target="_blank">assembly information</a> page.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/calJac3/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#marmoset">Downloads</a> page. See the WUSTL +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/calJac3/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#marmoset">Downloads</a> page. See the WUSTL Genome Center's <a href="http://genome.wustl.edu/data/data_use_policy" target="_blank">data use policy</a> for conditions of use.</p> <p> Many thanks to the Genome Center at WUSTL School of Medicine for providing the assembly data. The calJac3 annotation tracks were generated by UCSC and collaborators. See the <a href="credits.html#marmoset_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="051210"></a> <h2>May 12, 2010 Pig Genome Browser released</h2> <p> We have released a Genome Browser for the pig, Sus scrofa. This assembly (SGSC Sscrofa9.2 (<a href="https://www.ncbi.nlm.nih.gov/sites/entrez?Db=genomeprj&cmd=ShowDetailView&TermToSearch=10718" target="_blank">NCBI project 10718</a>, <a href="ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Sus_scrofa/Sscrofa9.2/" @@ -16767,32 +16767,32 @@ The pig is a member of the artiodactyls (cloven-hoofed mammals), which is an evolutionary clade distinct from the primates and rodents. It is an important model for human health, particularly for understanding complex traits such as obesity and cardiovascular disease. There is extensive conserved homology with the human genome.</p> <p> The pig genome assembly is a hybrid of BAC end-sequencing to anchor contigs combined with whole-genome shotgun (WGS) libraries. There are 19 chromosomes: chr1 - chr18, chrX and the mitochondrial sequence chrM (GenBank accession number NC_012095) for a total sequence length of 2,262,501,571 bases. There are 31,203,023 "N" bases in gaps, leaving 2,231,298,548 ACGT bases. For more information, see the Sanger Institute's <a href="http://www.sanger.ac.uk/Projects/S_scrofa/" target="_blank">Porcine Genome Sequencing Project</a> web page.</p> <p> Many thanks to the Swine Genome Sequencing Consortium and the Wellcome Trust Sanger Institute for the pig assembly data. Bulk downloads of the sequence and annotation data are available via the -Genome Browser <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/susScr2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#pig">Downloads</a> page. These data have +Genome Browser <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/susScr2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#pig">Downloads</a> page. These data have <a href="credits.html#pig_use">specific conditions for use</a>. The pig browser annotation tracks were generated by UCSC and collaborators worldwide. The UCSC Pig browser was produced by: Hiram Clawson, Brian Raney, Mark Diekhans, and Mary Goldman. See the <a href="credits.html#pig_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="050610"></a> <h2>May 6, 2010 UCSC hosts portal for Neandertal sequence, alignments, and analyses</h2> <p> In conjunction with the publication of the paper Green <em>et al.</em> <a href="http://www.sciencemag.org/cgi/content/full/328/5979/710" target="_blank">A Draft Sequence of the Neandertal Genome</a> in the May 7 issue of <em>Science</em>, the UCSC Genome Browser project has released a public <a href="../Neandertal">Neandertal portal</a> that may be used to access the Neandertal sequence, alignments to the UCSC hg18 (NCBI Build 36) human reference assembly and the @@ -16827,133 +16827,133 @@ <h2>Apr. 26, 2010 European Rabbit Genome Browser released</h2> <p> We have released a Genome Browser for the European rabbit, <em>Oryctolagus cuniculus</em>. This assembly (UCSC version oryCun2, Broad oryCun2) was produced by the <a href="http://www.broadinstitute.org/" target="_blank">Broad Institute of MIT and Harvard</a>, Cambridge, MA. The European rabbit is the precursor of all domestic rabbits. It is a valuable model in both immunology and evolutionary biology.</p> <p> The genome has been sequenced to nearly 7.5X coverage. The sequence is 2.7 Gb in length and includes 21 autosomes, the X chromosome, and the mitochondrial DNA (chrM), as well as 3,219 unplaced segments. For more information on the assembly, see the <a href="http://www.broadinstitute.org/science/projects/mammals-models/rabbit/rabbit-genome-sequencing-project" target="_blank">Rabbit Genome Project</a> page.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/oryCun2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#rabbit">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/oryCun2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#rabbit">Downloads</a> page. These data have <a href="credits.html#rabbit_use">specific conditions for use</a>.</p> <p> Many thanks to the Broad Institute for the rabbit assembly data. The oryCun2 annotation tracks were generated by UCSC and collaborators. We'd also like to acknowledge the UCSC Rabbit browser team: Hiram Clawson and Antonio Coelho. See the <a href="credits.html#rabbit_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="041610"></a> <h2>Apr. 16, 2010 Giant Panda Genome Browser released</h2> <p> We have released a Genome Browser for the giant panda, <em>Ailuropoda melanoleuca</em>. This assembly (UCSC version ailMel1, BGI AilMel1) was produced by the <a href="http://www.genomics.cn/en/index" target="_blank">Beijing Genomics Institute at Shenzhen</a>, Shenzhen, China. The panda is a member of Ursidae, despite earlier taxonomy that marked it as a relative of the raccoon. It has become the most recognized symbol for the fight for animal conservation.</p> <p> This draft of the panda genome has a size of approximately 2.3 Gb at 94% coverage. The assembly comprises 81,467 scaffolds and chrM (mitochondrial DNA). For more information on the assembly, see the BGI <a href="http://panda.genomics.org.cn/page/panda/index.jsp" target="_blank">Giant Panda Database</a> page.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/ailMel1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#panda">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/ailMel1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#panda">Downloads</a> page. These data have <a href="credits.html#panda_use">specific conditions for use</a>.</p> <p> Many thanks to the Beijing Genomics Institute at Shenzhen for the panda assembly data. The ailMel1 annotation tracks were generated by UCSC and collaborators. We'd also like to acknowledge the UCSC Panda browser team: Hiram Clawson, Ann Zweig, and Antonio Coelho. See the <a href="credits.html#panda_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="032410"></a> <h2>Mar. 24, 2010 African Savannah Elephant Genome Browser released</h2> <p> We have released a Genome Browser for the African savannah elephant, <em>Loxodonta africana</em>. This assembly (UCSC version loxAfr3, Broad loxAfr3) was produced by the <a href="http://www.broadinstitute.org/" target="_blank">Broad Institute</a>, Cambridge, MA, USA. The elephant was the first member of Afrotheria to be sequenced. Afrotheria is the deepest node of Eutheria, and the elephant sequence should be useful in reconstructing the ancestral eutherian genome.</p> <p> This draft of the elephant genome has a size of approximately 3 Gb with 7X coverage. The assembly comprises 2352 scaffolds and chrM (mitochondrial DNA). For more information on the assembly, see the Broad Institute <a href="http://www.broadinstitute.org/science/projects/mammals-models/elephant/elephant" target="_blank">Elephant Genome Project</a> page.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/loxAfr3/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#elephant">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/loxAfr3/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#elephant">Downloads</a> page. These data have <a href="credits.html#elephant_use">specific conditions for use</a>.</p> <p> Many thanks to the Broad Institute for the elephant assembly data. The loxAfr3 annotation tracks were generated by UCSC and collaborators. We'd also like to acknowledge the UCSC Elephant browser team: Hiram Clawson, Pauline Fujita, Vanessa Swing, Antonio Coelho, and Donna Karolchik. See the <a href="credits.html#elephant_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="031910"></a> <h2>Mar. 19, 2010 California Sea Hare Genome Browser released</h2> <p> We have released a Genome Browser for the California sea hare, <em>Aplysia californica</em>. This assembly (UCSC version aplCal1, Broad version Aplcal2.0) was produced by the <a href="http://www.broadinstitute.org/" target="_blank">Broad Institute</a>, Cambridge, MA, USA. The sea hare is the first mollusc to be sequenced, and is particularly noted for its nervous system, which is quite useful for neurobiological experimentation.</p> <p> This draft of the sea hare genome has a size of approximately 712 Mb with nearly 10X coverage. The assembly comprises 8766 scaffolds and chrM (mitochondrial DNA). For more information on the assembly, see the Broad Institute <a href="http://www.broadinstitute.org/science/projects/mammals-models/vertebrates-invertebrates/aplysia/aplysia-genome-sequencing-project" target="_blank">Aplysia Genome Project</a> page.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/aplCal1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#seahare">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/aplCal1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#seahare">Downloads</a> page. These data have <a href="credits.html#seahare_use">specific conditions for use</a>.</p> <p> Many thanks to the Broad Institute for the sea hare assembly data. The aplcal1 annotation tracks were generated by UCSC and collaborators. We'd also like to acknowledge the UCSC Sea Hare browser team: Galt Barber, Brian Raney, Hiram Clawson, Katrina Learned, Antonio Coelho, and Donna Karolchik. See the <a href="credits.html#seahare_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="031210"></a> <h2>Mar. 12, 2010 Updated Tetraodon Genome Browser available</h2> <p> We have released a Genome Browser for the latest assembly of <em>Tetraodon nigroviridis</em>. The V8 assembly (March 2007, UCSC version tetNig2) was provided by <a href="http://www.genoscope.cns.fr/" target="_blank">Genoscope</a>, Evry, France, in collaboration with the <a href="http://www.broad.mit.edu/annotation/tetraodon/background.html" target="_blank">Broad Institute</a>, Cambridge, MA, USA. For detailed sequencing and assembly information, see the Genoscope <em>Tetraodon nigroviridis</em> <a href="http://www.genoscope.cns.fr/spip/Tetraodon-nigroviridis-whole.html" target="_blank">assembly</a> page.</p> <p> Downloads of the Tetraodon data and annotations may be obtained from the UCSC -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/tetNig2/" target="_blank">FTP site</a> or -<a href=http://hgdownload.soe.ucsc.edu/downloads.html#tetraodon>Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/tetNig2/" target="_blank">FTP site</a> or +<a href=http://hgdownload.gi.ucsc.edu/downloads.html#tetraodon>Downloads</a> page. These data have been freely provided by Genoscope for use in the UCSC Genome Browser with <a href="credits.html#tetraodon_use" target="_blank">specific conditions for use</a>. For more information about the <em>Tetraodon nigroviridis</em> project, see the Genoscope <a href="http://www.genoscope.cns.fr/spip/-Tetraodon-nigroviridis,387-.html" target="_blank">website</a>.</p> <p> Many thanks to Genoscope and the Broad Institute for providing these data. The tetNig2 annotation tracks were generated by UCSC and its collaborators. We'd also like to acknowledge the UCSC Tetraodon browser team, which includes several new faces: Hiram Clawson, Mark Diekhans, Brian Raney, Ann Zweig, Mary Goldman, Vanessa Swing, Antonio Coelho, Robert Kuhn, and Donna Karolchik. See the <a href="credits.html#tetraodon_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="022410"></a> <h2>Feb. 24, 2010 New gene name search functionality released</h2> @@ -17012,32 +17012,32 @@ <p> The most recent zebrafish assembly -- zv8 (UCSC version danRer6, Dec. 2008) -- is now available in the UCSC Genome Browser. This assembly was produced by the Wellcome Trust Sanger Institute, UK.</p> <p> The danRer6 assembly consists of nearly 1.5 billion bp in 11,623 scaffolds with a coverage of 6.5-7x. It includes sequence anchored to chromosomes 1-25 and chrM (mitochondrial), as well as 11,418 unplaced scaffolds. Significant problems existing in previous assemblies have been rectified in this assembly through the use of a whole-genome shotgun assembly with more coverage and a reorganization of the fingerprint contig order and orientation through more careful use of maps. For more information about this assembly, see the Sanger Institute web page for the <a href="http://www.sanger.ac.uk/Projects/D_rerio/Zv8_assembly_information.shtml" target="_blank"><em>Danio rerio</em> Sequencing Project</a> and the track description page for the danRer6 Assembly track.</p> <p> The danRer6 sequence and annotation data can be downloaded from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/danRer6/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#zebrafish">downloads</a> page. Please review +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/danRer6/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#zebrafish">downloads</a> page. Please review the <a href="http://www.sanger.ac.uk/notices/use-policy.shtml" target="_blank">guidelines</a> for using these data.</p> <p> We'd like to thank the Wellcome Trust Sanger Institute for providing this assembly. The UCSC zebrafish Genome Browser was produced by Galt Barber, Robert Kuhn, Katrina Learned, and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the <a href="credits.html#zebrafish_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to the release of this browser.</p> <!-- ============= 2009 archived news ============= --> <a name="2009"></a> <a name="121409"></a> <h2>Dec. 14, 2009 New job posting: Biological Data Technician</h2> <p> @@ -17094,86 +17094,86 @@ Testing/User Support Technician</a> on the Center for Biomolecular Science and Engineering (CBSE) website. For detailed job descriptions and application information, go to the <a href="http://jobs.ucsc.edu/" target="_blank">UCSC Staff Employment website</a>, click the "Search Postings" link on the sidebar, and type in job #0902365 (Testing/User Support Technician).</p> <a name="090909"></a> <h2>Sep. 9, 2009 Changes to the bigBed/bigWig data formats</h2> <p> If you have been taking advantage of the new bigBed format (for very large data sets), you'll be happy to hear that we have considerably slimmed down the memory footprint of the program that converts BED files into bigBed files: bedToBigBed. Because it now uses a multi-pass approach, it now takes only 1/4 the amount of RAM as the size of the uncompressed BED input file (instead of the 5x RAM it needed previously!). Read more <a href="help/bigBed.html">here</a>. Pick up the new bedToBigBed executable -<a href="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/">here</a>.</p> +<a href="http://hgdownload.gi.ucsc.edu/admin/exe/linux.x86_64/">here</a>.</p> <p> In conjunction with this change, there is also a change to the way you must specify your bigBed or bigWig custom track. When you specify the location of your local bigBed/bigWig file (on your web-accessible http, https, or ftp server), use the designation "bigDataUrl" instead of the old "dataUrl":</p> <pre><code>track type=bigBed name="My Big Bed" description="Some Data from My Lab" <strong>bigDataUrl</strong>=http://myorg.edu/mylab/myBigBed.bb</code></pre> <p> Additionally, we would like to announce a companion program to the previously-announced wigToBigWig program: bedGraphToBigWig. This program converts bedGraph files into bigWig files. The bedGraph format allows display of sparse or varying-size data. Read more <a href="help/bigWig.html">here</a>. You can download the new bedGraphToBigWig utility -<a href="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/">here</a>.</p> +<a href="http://hgdownload.gi.ucsc.edu/admin/exe/linux.x86_64/">here</a>.</p> <p> The main advantage of the bigBed and bigWig formats is that only the portions of the files needed to display a particular region are transferred to UCSC, so for large data sets, displaying bigBed/bigWig data is considerably faster than regular BED/wig data. The bigBed/bigWig file remains on your web accessible server (http, https, or ftp), not on the UCSC server. Consequently, creating your custom track is very fast. Only the portion that is needed for the chromosomal position you are currently viewing is locally cached at UCSC as a "sparse file".</p> <a name="081009"></a> <h2>Aug. 10, 2009 Updated Yeast Genome Browser released</h2> <p> We have added the June 2008 release of the yeast genome (<em>Saccharomyces cerevisiae</em>) based on sequence from the <a href="http://www.yeastgenome.org/" target="_blank">Saccharomyces Genome Database</a> (SGD). The sequence, open reading frame (ORF), and gene annotations were downloaded from the site <a href="ftp://genome-ftp.stanford.edu/pub/yeast/data_download" target="_blank">ftp://genome-ftp.stanford.edu/pub/yeast/data_download</a>.</p> <p> The S288C strain was used in this sequencing project. Reference information for each chromosome may be found in the SGD <a href="http://www.yeastgenome.org/chromosomes.shtml" target="_blank">Systematic Sequencing Table</a>. Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/sacCer2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#yeast">Downloads</a> page.</p> +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/sacCer2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#yeast">Downloads</a> page.</p> <p> See the <a href="credits.html#yeast_credits">Credits</a> page for details on contributions to this release.</p> <a name="072209"></a> <h2>Jul. 22, 2009 Updated Opossum Genome Browser released</h2> <p> We have released an updated opossum (<em>Monodelphis domestica</em>) genome browser, UCSC version monDom5, corresponding to the <a href="http://www.broad.mit.edu/mammals/opossum/" target="_blank">Broad Institute's</a> October 2006 assembly.</p> <p> This draft of the opossum genome has approximately 6.8X coverage. The assembly length is nearly 3.61 billion bp including gaps (3.50 billion bp without gaps) contained on chromosomes 1-8, X, M (mitochondrial DNA), and Un (unmapped clone contigs). The N50 of the scaffolds including gaps is 60,456 kb; the N50 without gaps is 110 kb.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/monDom5/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#opossum">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/monDom5/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#opossum">Downloads</a> page. These data have <a href="../goldenPath/credits.html#opossum_use">specific conditions for use</a>.</p> <p> Many thanks to The Broad Institute for the opossum assembly data. The monDom5 annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="../goldenPath/credits.html#opossum_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="070709"></a> <h2>Jul. 7, 2009 Engineering job opening with UCSC Genome Browser project</h2> <p> The UCSC Center for Biomolecular Science and Engineering is currently accepting applications for a full-time, experienced engineer to develop software and databases for the UCSC Genome Browser and related projects. The successful candidate must be independent, articulate, self-motivated, able to learn and integrate technical information quickly, and have a strong commitment to quality and best engineering practices.</p> @@ -17325,55 +17325,55 @@ <h2>Dec. 3, 2008 Updated Horse Genome Browser available</h2> <p> The Sep. 2007 EquCab2 release of the horse genome (Equus caballus) is now available in the UCSC Genome Browser. This assembly, UCSC version equCab2, was produced by the <a href="http://www.broad.mit.edu/" target="_blank">Broad Institute</a>. </p> <p> The horse draft genome has been sequenced to 6.8X coverage. Approximately 84% of the sequence has been anchored to chromosomes, which include autosomes 1-31 and sex chromosome X. Unanchored contigs that could not be localized to a chromosome have been concatenated into the virtual chromosome "chrUn", separated by gaps of 1,000 bp. The mitochondrial sequence is also available in the Genome Browser as the virtual chromosome "chrM". <p>For more details about the current assembly, see the Broad Institute <a href="http://www.broad.mit.edu/mammals/horse/" target="_blank">Horse Genome Project</a> page.</p> <p> Bulk downloads of the sequence and annotation data are available from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/equCab2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#horse">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/equCab2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#horse">Downloads</a> page. These data have <a href="credits.html#horse_use">specific conditions for use</a>.</p> <p> The UCSC Horse Genome Browser was produced by Larry Meyer, Hiram Clawson, Pauline Fujita, Brooke Rhead, and Donna Karolchik. See the <a href="credits.html#horse_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="110708"></a> <h2>Nov. 7, 2008 Medaka Genome Browser updated</h2> <p> We have updated the initial UCSC Medaka Genome Browser (oryLat1) to correct an error with chrUn in which the gap relationships between the contigs within their ultracontigs were incorrect. This error was introduced by UCSC during the browser assembly process. The corrected replacement browser, oryLat2 (Oct. 2005), is based on the same v1.0 assembly produced by the National Institute of Genetics (NIG) and the University of Tokyo, Japan. We have removed the original oryLat1 assembly from the browser.</p> <a name="091708"></a> <h2>Sep. 17, 2008 Seven assemblies archived</h2> <p> We have archived seven older assemblies of the human (hg15), mouse (mm5, mm6), rat (rn2), <em>C. elegans</em> (ce1), zebrafish (danRer2), and cow (bosTau1) genomes. You can continue to download these assemblies from the Genome Browser -<a href ="http://hgdownload.soe.ucsc.edu/downloads.html">downloads server</a>. At least two later +<a href ="http://hgdownload.gi.ucsc.edu/downloads.html">downloads server</a>. At least two later assemblies for each of these organisms remain available on the main Genome Browser site.</p> <p> We do not provide blat servers or updated GenBank data for archived assemblies. However, it is still possible to lift coordinates between these assemblies and those on the main browser site.</p> <a name="091508"></a> <h2>Sep. 15, 2008 Request for input on ENCODE data release plan</h2> <p> The National Human Genome Research Institute (NHGRI) has updated the data release plan for the <a href="http://www.genome.gov/ENCODE" target="_blank">ENCODE</a> and model organism ENCODE (<a href="http://www.genome.gov/modENCODE" target="_blank">modENCODE</a>) projects. Because the plan is intended to take into account the needs and responsibilities of the resource users, NHGRI is soliciting feedback on the proposal from the research community before the plan is finalized. To facilitate this review, UCSC has made the plan available to the community <a href="../encodeDCC/ENCODE_Consortia_Data_Release_Policy_2008-09-11.doc">here</a> on our ENCODE @@ -17422,160 +17422,160 @@ collection of vertebrate genome browsers. The v3.2.4 draft assembly (UCSC version taeGut1) was produced by the Genome Sequencing Center at the Washington University in St. Louis (WUSTL) School of Medicine in St. Louis, MO, USA.</p> <p> The zebra finch genome is the second bird genome to be sequenced (following the chicken, <em>Gallus gallus</em>). The DNA used for the shotgun sequencing and the BAC and cosmid libraries was derived from a single male zebra finch. The initial assembly was generated using PCAP with approximately 6X coverage. About 1.0 Gb of the 1.2-Gb genome has been ordered and oriented along 33 chromosomes and one linkage group. The chromosome names are based on their homologous chromosomes in the chicken (<em>Gallus gallus</em>). For more assembly details, as well as a cross reference table of zebra finch and chicken chromosome names, see the WUSTL <a href="http://genome.wustl.edu/pub/organism/Other_Vertebrates/Taeniopygia_guttata/assembly/Taeniopygia_guttata-3.2.4/ASSEMBLY" target="_blank">assembly notes</a>.</p> <p> Bulk downloads of the sequence and annotation data are available from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/taeGut1/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#zebrafinch">Downloads</a> page. These data +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/taeGut1/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#zebrafinch">Downloads</a> page. These data have <a href="credits.html#zebrafinch_use">specific conditions for use</a>. Please refer to the WUSTL <a href="http://genome.wustl.edu/data.cgi" target="_blank">data use policy</a> for additional usage guidelines and citation information.</p> <p> The UCSC Zebra Finch Genome Browser and initial annotations were produced by Brian Raney, Kayla Smith, Pauline Fujita, and Donna Karolchik. See the <a href="credits.html#zebrafinch_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release. </p> <a name="072208"></a> <h2>Jul. 22, 2008 Updated <em>C. elegans</em> Browser released</h2> <p> Culminating our recent updates of the nematode browsers on our site, we've released a Genome Browser for the latest <em>C. elegans</em> assembly based on sequence version WS190 deposited into WormBase in May 2008. This new assembly (UCSC version ce6) was produced jointly by the Wellcome Trust Sanger Institute in Hinxton, England, and the Genome Sequencing Center at Washington University in St. Louis (WUSTL) School of Medicine, MO, USA. The ce6 browser includes a Conservation annotation and pairwise alignment tracks comparing <em>C. elegans</em> sequence with that of five other worms.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/ce6">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#c_elegans">Downloads</a> page. Please +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/ce6">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#c_elegans">Downloads</a> page. Please review the WUSTL <a href="http://genome.wustl.edu/data.cgi" target="_blank">data use policy</a> for usage restrictions and citation information.</p> <p> We'd like to thank WUSTL and the Sanger Institue for providing the sequence data for this assembly. The UCSC ce6 browser was produced by Hiram Clawson, Kayla Smith, Pauline Fujita, Brooke Rhead, and Donna Karolchik. See the Genome Browser <a href="credits.html#worm_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release. </p> <a name="062608"></a> <h2>Jun. 26, 2008 New Worm Genome available</h2> <p> Along with the set of worm browser updates that we're currently releasing, we've added a new nematode to the collection: <em>Caenorhabditis japonica</em>. This genome assembly (UCSC version caeJap1, Mar. 2008) corresponds to the v. 3.0.2 assembly produced by the Genome Sequencing Center at the Washington University St. Louis (WUSTL) School of Medicine.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/caeJap1">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#caeJap">Downloads</a> page. Please review the +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/caeJap1">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#caeJap">Downloads</a> page. Please review the WUSTL <a href="http://genome.wustl.edu/data.cgi" target="_blank">data use policy</a> for usage restrictions and citation information.</p> <p> We'd like to thank WUSTL for providing the sequence data for this assembly. The UCSC caeJap1 browser was produced by Hiram Clawson, Ann Zweig, and Donna Karolchik. See the Genome Browser <a href="credits.html#worm_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="062008"></a> <h2>Jun. 20, 2008 Two worm updates released</h2> <p> We've updated our browsers for the <em>C. remanei</em> and <em>C. brenneri</em> nematode genomes. Both sets of sequence were obtained from the Genome Sequencing Center at Washington University in St. Louis (WUSTL) School of Medicine. The <em>C. remanei</em> assembly (UCSC version caeRem3) corresponds to WUSTL version 15.0.1 dated May 2007. The <em>C. brenneri</em> assembly (UCSC version caePb2) is based on WUSTL version 6.0.1 dated Feb. 2008.</p> <p>Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html">Downloads</a> page. Please review the WUSTL +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html">Downloads</a> page. Please review the WUSTL <a href="http://genome.wustl.edu/data.cgi" target="_blank">data use policy</a> for usage restrictions and citation information.</p> <p> We'd like to thank WUSTL for providing the sequence data for these assemblies. The UCSC worm browsers were produced by Hiram Clawson, Brooke Rhead, Pauline Fujita, and Donna Karolchik. See the Genome Browser <a href="credits.html#worm_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="061008b"></a> <h2>Jun. 10, 2008 Lamprey Browser released</h2> <p> We have released a Genome Browser for the Mar. 2007 assembly of the lamprey genome, <em>Petromyzon marinus</em>. This assembly, UCSC version petMar1, was produced by the Genome Sequencing Center at the Washington University in St. Louis School of Medicine (WUSTL), St. Louis, MO, USA.</p> <p> Bulk downloads of the sequence and annotation data are available from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/petMar1/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#lamprey">Downloads</a> page. The lamprey +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/petMar1/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#lamprey">Downloads</a> page. The lamprey sequence is made freely available before scientific publication. Please see the WUSTL <a href="http://genome.wustl.edu/data.cgi" target="_blank">data use policy</a> for usage restrictions and citation information.</p> <p> The UCSC Lamprey Genome Browser was produced by Hiram Clawson, Ann Zweig, Pauline Fujita, and Donna Karolchik. See the <a href="credits.html#lamprey_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release. </p> <a name="061008a"></a> <h2>Jun. 10, 2008 Lancelet genome available in browser</h2> <p> The Mar. 2006 release of the lancelet genome (<em>Branchiostoma floridae</em>) is now available in the UCSC Genome Browser. This assembly, UCSC version braFlo1, was produced by the <a href="http://genome.jgi-psf.org/Brafl1/Brafl1.info.html" target="_blank">DOE Joint Genome Institute</a> (JGI), Walnut Creek, CA, USA.</p> <p> Bulk downloads of the sequence and annotation data are available from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/braFlo1/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#lancelet">Downloads</a> page. The lancelet +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/braFlo1/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#lancelet">Downloads</a> page. The lancelet sequence is made freely available before scientific publication. Please see the JGI <a href="http://genome.jgi-psf.org/Brafl1/Brafl1.download.html" target="_blank">data release policy</a> for usage restrictions and citation information.</p> <p> The UCSC Lancelet Genome Browser was produced by Hiram Clawson, Ann Zweig, Pauline Fujita, and Donna Karolchik. See the <a href="credits.html#lancelet_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release. </p> <a name="060508"></a> <h2>Jun. 5, 2008 Guinea Pig Browser released</h2> <p> The Feb. 2008 CavPor3 release of the guinea pig genome (<em>Cavia porcellus</em>) is now available in the UCSC Genome Browser. This assembly, UCSC version cavPor3, was produced by the <a href="http://www.broad.mit.edu/" target="_blank">Broad Institute</a>.</p> <p> The guinea pig is one of 24 mammals whose genomes are being sequenced as part of the <a href="http://www.broad.mit.edu/mammals/" target="_blank">Mammalian Genome Project</a>, funded by the National Institutes of Health. While most of these genomes are slated for low-coverage (2X), a limited subset (including the guinea pig genome) are being sequenced to a higher quality of 6-7X.</p> <p> The guinea pig genome has been sequenced to 6.76X coverage with 95.55% of bases assembled. A total of 3143 scaffolds cover 2,722,377,657 bases (2.17% in gaps), with 50% of the scaffolds having a (N50) length of at least 27,408,292 bases (not including gaps). For more details about the assembly, see the Broad Institute <a href="http://www.broad.mit.edu/mammals/" target="_blank">Mammmalian Genome Project</a> page.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/cavPor3/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#guineapig">Downloads</a> page. These data +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/cavPor3/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#guineapig">Downloads</a> page. These data have <a href="credits.html#guineapig_use">specific conditions for use</a>. </p> <p> The UCSC Guinea Pig Genome Browser was produced by Tim Dreszer, Kate Rosenbloom, Hiram Clawson, Kayla Smith, Robert Kuhn, and Donna Karolchik. See the <a href="credits.html#guineapig_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="050508"></a> <h2>May 5, 2008 GSID HIV data browser now available</h2> <p> Global Solutions for Infectious Diseases (GSID) has announced the launch of an HIV Data Browser with clinical and viral sequence data from infected subjects in the VAX004 (North American/European) Phase III clinical trial of the AIDSVAX B/B vaccine. The browser, which is a customized version of the UCSC Genome Browser developed by the UCSC Genome Bioinformatics group and hosted by GSID, provides researchers with searchable demographic and clinical data from volunteers who became HIV @@ -17606,32 +17606,32 @@ has contributed to the study of brain function, immunity, reproductive biology and drug toxicity. <em>C. jacchus</em> marmosets typically give birth to twins that are somatic chimeras, i.e. each sibling is the mixture of sibling genotypes. (Excerpted from the WUSTL <em>C. jacchus</em> <a href="http://genome.wustl.edu/genome.cgi?GENOME=Callithrix%20jacchus" target="_blank">project</a> page.)</p> <p> The <em>C. jacchus</em> genome was sequenced to 6X coverage using DNA from a female marmoset provided by the Southwestern National Primate Research Center in San Antonio, TX, USA. DNA from a full brother of the female was used as the source for the CHORI-259 BAC library. This assembly is composed of 49,724 supercontigs containing a total of approximately 3.02 billion bases. For more statistics and details on the assembly process, refer to the WUSTL Callithrix_jacchus-2.0.2 <a href="http://genome.wustl.edu/pub/organism/Primates/Callithrix_jacchus/assembly/Callithrix_jacchus-2.0.2/ASSEMBLY" target="_blank">assembly</a> page.</p> <p> Bulk downloads of the calJac1 sequence and annotations may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/calJac1/" target="_blank">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#marmoset">Downloads</a> page. The sequence +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/calJac1/" target="_blank">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#marmoset">Downloads</a> page. The sequence data can also be obtained directly from <a href="http://genome.wustl.edu/pub/organism/Primates/Callithrix_jacchus/assembly/Callithrix_jacchus-2.0.2/" target="_blank">WUSTL</a>. See the WUSTL <a href="http://genome.wustl.edu/data.cgi" target="_blank">data use policy</a> for conditions of use. Please acknowledge WUSTL School of Medicine Genome Sequencing Center in any publications that result from the use of this sequence assembly.</p> <p> We'd like to thank WUSTL School of Medicine Genome Sequencing Center for providing this assembly. The initial set of marmoset browser annotation tracks were generated by UCSC. The UCSC marmoset Genome Browser team is Hiram Clawson, Robert Kuhn, Pauline Fujita, Brooke Rhead, and Donna Karolchik. See the <a href="credits.html#marmoset_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="041508"></a> <h2>Apr. 15, 2008 Introducing the Archaeal Genome Browser Database</h2> <p> @@ -17676,32 +17676,32 @@ as "chrM") was obtained from GenBank accession GI:60101824.</p> <p> The Btau_4.0 assembly was tested against available bovine sequence data sets (EST sequences and finished BAC sequences) for extent of coverage (completeness). When assembled contigs were tested, over 95% of the sequences in these data sets were found to be represented, indicating that the shotgun libraries used to sequence the genome were comprehensive. Of the 1.04 million EST sequences 95.0% were contained in the assembled contigs. Assuming the ESTs are uniformly distributed throughout the genome, the estimated genome size is 2.73Gb/95% = 2.87Gb. For detailed information on the sequencing and assembly techniques, see the Baylor <a href="http://www.hgsc.bcm.tmc.edu/projects/bovine/" target="_blank">Bovine Genome Project</a> web page.</p> <p> For a list of the chromosomes and scaffolds in this assembly, click the "Sequences" link on the cow browser <a href="../cgi-bin/hgGateway?db=bosTau4">gateway</a> page.</p> <p>Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/bosTau4">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#cow">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/bosTau4">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#cow">Downloads</a> page. These data have <a href="http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html" target="_blank">specific conditions for use</a>. The cow annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> We'd like to thank Baylor College of Medicine for providing this assembly. The UCSC bosTau4 browser and documentation were produced by Hiram Clawson, Brian Raney, and Ann Zweig. See the <a href="credits.html#cow_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="032408"></a> <h2>Mar. 24, 2008 Free Genome Browser institutional seminars</h2> <p> The UCSC Bioinformatics Group announces your chance to bring our hands-on computer workshop on the UCSC Genome Browser to your institution. The seminar is presented by our training partner, <a href="http://www.openhelix.com" target="_blank">OpenHelix</a>.</p> @@ -17748,32 +17748,32 @@ "Susie" from the Gladys Park Zoo (Brownsville, TX, USA). The combined sequence reads were assembled using <a href="http://www.genome.org/cgi/content/abstract/13/9/2164" target="_blank">PCAP</a> and filtered for all known non-orangutan sequence contaminants. For more details about the assembly, see the orangutan browser <a href="../cgi-bin/hgGateway?db=ponAbe2">gateway</a> page and the WUSTL <a href="http://genome.wustl.edu/genome.cgi?GENOME=Pongo%20abelii" target="_blank"><em>Pongo abelii</em></a> web page.</p> <p> Of the 3.09 Gb of total sequence, 3.08 Gb are ordered and oriented along the chromosomes. Gap sizes between supercontigs were estimated based on their size in human, with a maximum gap size of 30 kb allowed. For a list of the chromosomes in this assembly, click the "Sequences" link on the orangutan browser <a href="../cgi-bin/hgGateway?db=ponAbe2">gateway</a> page. The mitochondrial sequence is also available as the virtual chromosome "chrM".</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/ponAbe2">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#orangutan">Downloads</a> page. These data +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/ponAbe2">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#orangutan">Downloads</a> page. These data have <a href="credits.html#orangutan_use">specific conditions for use</a>. The orangutan browser annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> We'd like to thank WUSTL for providing this assembly. The UCSC ponAbe2 browser and documentation were produced by Hiram Clawson, Kayla Smith, Robert Kuhn, Ann Zweig and Donna Karolchik. See the <a href="credits.html#orangutan_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="030708"></a> <h2>Mar. 7, 2008 New reverse functionality released</h2> <p> The Genome Browser team is happy to announce new functionality in the main Genome Browser track display. A new configuration button, "Reverse," now allows users to view the entire browser image flipped right-to-left. This is especially useful when a user's gene of interest aligns on the opposite strand from the reference assembly. Those genes then appear in the 5' to 3' @@ -17824,32 +17824,32 @@ UCSC Genome Browser. The Zv7 assembly was produced by The Wellcome Trust Sanger Institute in collaboration with the Max Planck Institute for Developmental Biology in Tuebingen, Germany, and the Netherlands Institute for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands.</p> <p> This assembly consists of 1,440,582,308 bp in 5,036 fragments. It includes sequence anchored to chromosomes 1-25 and chrM (mitochondrial), as well as 5010 unplaced scaffolds. The assembly was produced by integrating finished clone sequence from the physical map with whole genome shotgun assembly sequence. The N50 size is 1,153,933, n = 277 (i.e. the length such that 50% of the assembled genome lies in blocks of the N50 size or longer). For more information about this assembly, see the Sanger Institute web page for the <a href="http://www.sanger.ac.uk/Projects/D_rerio/Zv7_assembly_information.shtml" target="_blank"><em>Danio rerio</em> Sequencing Project</a> and the track description page for the Assembly track.</p> <p> The danRer5 sequence and annotation data can be downloaded from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/danRer5/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#zebrafish">downloads</a> page. Please review +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/danRer5/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#zebrafish">downloads</a> page. Please review the <a href="http://www.sanger.ac.uk/notices/use-policy.shtml" target="_blank">guidelines</a> for using these data.</p> <p> We'd like to thank the Wellcome Trust Sanger Institute, the Max Planck Institute for Developmental Biology, Hubrecht Laboratory and the other institutions who contributed to the sequencing and mapping effort of this release. Special thanks to the Zebrafish Genome Initiative at Children's Hospital in Boston for their collaboration on this release. The UCSC zebrafish Genome Browser was produced by Rachel Harte, Ann Zweig, and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the <a href="credits.html#zebrafish_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to the release of this browser.</p> <a name="101007"></a> <h2>10 Oct. 10, 2007 New Browser for Purple Sea Urchin</h2> <p> @@ -17867,138 +17867,138 @@ <p> Compared to previous sea urchin releases, the Spur_2.1 assembly is more continuous and has fewer false duplications; contaminations identified in the previous Spur_2.0 assembly have been removed. This draft assembly may contain errors; therefore, users should exercise caution. Typical errors may include misassemblies of repeat sequences, collapses of repeat regions, and artificial duplications in polymorphic regions. However, base accuracy in contigs is usually very high with most errors near the ends of contigs.</p> <p> More assembly details can be found in the <a href="ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Spurpuratus/fasta/Spur_v2.1/README_Spur_v2.1.txt" target="_blank">Spur_2.1 README file</a> and on the BCM HGSC <a href="http://www.hgsc.bcm.tmc.edu/projects/seaurchin/" target="_blank">Sea Urchin Genome Project</a> web page.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/strPur2">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#urchin">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/strPur2">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#urchin">Downloads</a> page. These data have <a href="http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html" target="_blank">specific conditions for use</a>. The initial set of strPur2 annotation tracks was generated by UCSC. See the <a href="credits.html#urchin_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release. </p> <a name="100407"></a> <h2>Oct. 4, 2007 ENCODE Genome Browser Released for hg18 Assembly</h2> <p> The UCSC ENCODE browser for the human genome assembly hg18 (NCBI Build 36) is now available. You can access the browser directly at <a href="../ENCODE/encode.hg18.html">http://genome.ucsc.edu/ENCODE/encode.hg18.html</a> or by clicking the ENCODE link in the sidebar menu on this page, then clicking the Regions (hg18) link in the sidebar menu on the ENCODE portal page.</p> <p> The hg18 ENCODE browser includes 540 data tables in 59 browser tracks that were migrated from the hg17 browser. The hg17 data coordinates were converted to hg18 coordinates using the UCSC liftOver process.</p> <p> To improve the accessibility of the data, related ENCODE tracks have been gathered into new configuration groupings ("super-tracks") that can be displayed or hidden using a single visiblity control. We have also reduced the number of track groups and have modified some of the group names for clarity. ENCODE tracks with whole-genome data have been moved into the standard browser track groups.</p> <p> For more information about the hg18 ENCODE data migration, see the News section on the UCSC <a href="../ENCODE/">ENCODE portal page</a> and the UCSC -<a href="http://genomewiki.soe.ucsc.edu/index.php/ENCODE_Hg18_Migration" +<a href="http://genomewiki.gi.ucsc.edu/index.php/ENCODE_Hg18_Migration" target="_blank">genomeWiki</a>.</p> <a name="082207b"></a> <h2>Aug. 22, 2007 New Mouse Browser released</h2> <p> The latest mouse genome assembly from the Mouse Genome Sequencing Consortium, NCBI Build 37.1, is now available in the UCSC Genome Browser. This version (UCSC version mm9) is considered to be essentially finished.</p> <p> The Build 37.1 assembly includes approximately 2.6 Gb of sequence on chromosomes 1-19, X, Y, M (mitochondrial DNA) and Un (unmapped clone contigs). In-depth information about this assembly will become available on the <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.16/" target="_blank">NCBI website</a>. On chromosome Y in this assembly, only the short arm has reliable mapping data; therefore, most of the contigs on the Y chromosome are unplaced.</p> <p> The mm9 sequence and annotation data may be downloaded from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/mm9/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/">Downloads</a> web page. The mm9 annotation +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/mm9/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/goldenPath/mm9/">Downloads</a> web page. The mm9 annotation tracks were generated by UCSC and collaborators worldwide. NOTE: To expedite the availability of the mm9 browser on our website, the initial release does not contain the comparative genomics annotations. These will be added to our website as they become available. Also, note that the UCSC mm9 database contains only the reference strain C57BL/6J.</p> <p> We'd like to thank Deanna Church and the Mouse Genome Sequencing Consortium for this assembly. We'd also like to acknowledge the work of the UCSC mm9 team: Hiram Clawson, Archana Thakkapallayil, Robert Kuhn, and Donna Karolchik. For a complete list of the individuals and organizations who participated in this assembly, see the <a href="credits.html#mouse_credits">Credits</a> page.</p> <a name="082207a"></a> <h2>Aug. 22, 2007 Latest Bovine assembly available</h2> <p> The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the Aug. 2006 Btau_3.1 draft assembly of the cow genome. This assembly (UCSC version bosTau3) was provided by Baylor College of Medicine Human Genome Sequencing Center in Houston, TX.</p> <p> The Btau_3.1 release was produced by the Atlas genome assembly system at Baylor College of Medicine Human Genome Sequencing Center. The sequencing strategy combined BAC shotgun reads with whole genome shotgun reads from small insert libraries as well as BAC end sequences. The assembly contains chromosomes 1-29 and X as well as 13045 scaffolds (named chrUn.003.*). More information on the Btau_3.1 assembly can be found on the Baylor <a href="http://www.hgsc.bcm.tmc.edu/projects/bovine/" target="_blank">Bovine Genome Project</a> web page and the <a href="ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Btaurus/fasta/Btau20060815-freeze/ReadMeBovine.3.1.txt" target="_blank">Readme</a> file that accompanies this release.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/bosTau3/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#cow">Downloads</a> page. Please refer to the +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/bosTau3/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#cow">Downloads</a> page. Please refer to the Baylor <a href="http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html" target="_blank">conditions of use</a> regarding these data. The bosTau3 annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> We'd like to thank Baylor College of Medicine for the bovine sequence and assembly. We'd also like to acknowledge the members of the UCSC Genome Bioinformatics Group who contributed to the Cow Genome Browser: Heather Trumbower, Angie Hinrichs, Kayla Smith, and Donna Karolchik. See the <a href="credits.html#cow_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="080207"></a> <Aug. 2, 2007 Five new worm assemblies</h2> <p> We've updated our existing nematode browsers--for <em>C. elegans</em> and <em>C. briggsae</em>--to the latest publicly available assemblies. In addition, we've added three new worms to our collection: <em>C. brenneri</em> (Caenorhabditis n. sp. PB2801), <em>C. remanei</em>, and <em>Pristionchus pacificus</em>. The <em>C. elegans</em> sequence was obtained from WormBase; the Genome Sequencing Center at Washington University in St. Louis (WUSTL) provided sequence data for the other four assemblies.</p> <table> <tr><th nowrap>SPECIES</th><th nowrap>UCSC VERSION</th><th nowrap>RELEASE DATE</th><th nowrap>SOURCE/RELEASE</th></tr> <tr><td><em>C. elegans</em></td><td>ce4</td><td>Jan. 2007</td><td>WormBase v. WS170</td></tr> <tr><td><em>C. briggsae</em></td><td>cb3</td><td>Jan. 2007</td><td>WUSTL Cb3</td></tr> <tr><td><em>C. brenneri</em></td><td>caePb1</td><td>Jan. 2007</td><td>WUSTL 4.0</td></tr> <tr><td><em>C. remanei</em></td><td>caeRem2</td><td>Mar. 2007</td><td>WUSTL 1.0</td></tr> <tr><td><em>P. pacificus</em></td><td>priPac1</td><td>Feb. 2007</td><td>WUSTL 5.0</td></tr> </table> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html">Downloads</a> page. Please review the +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html">Downloads</a> page. Please review the <a href="http://genome.wustl.edu/data.cgi" target="_blank">data use policy</a> for the WUSTL-generated assemblies. </p> <p> We'd like to thank WUSTL, WormBase, and the Sanger Institute for providing the sequence data for these assemblies. The UCSC worm browsers were produced by Hiram Clawson, Kayla Smith, Brooke Rhead, Ann Zweig, and Donna Karolchik. See the Genome Browser <a href="credits.html">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="071307"></a> <h2>Jul. 13, 2007 <em>Drosophila melanogaster</em> Release 5 now available in Genome Browser</h2> <p> The latest <em>D. melanogaster</em> assembly can now be viewed in the UCSC Genome Browser. This version -- Release 5, dated Apr. 2006 (UCSC version dm3) -- was provided by the <a href="http://www.fruitfly.org/" target="_blank">Berkeley Drosophila Genome Project</a> (BDGP) and combines both euchromatic and heterochromatic sequence. The Release 5.1 annotations (Mar. 2007) were @@ -18007,32 +18007,32 @@ The six euchromatic arms in this assembly were sequenced and assembled by BDGP from a combination of BAC and whole genome shotgun data, and have been finished to high quality. All euchromatic sequence have been compared to the restriction digest fingerprints in multiple enzymes for validity. The details of this analysis will be described in a forthcoming publication.</p> <p> Heterochromatic sequence from the <a href="http://www.fruitfly.org/" target="_blank">Drosophila Heterochromatin Genome Project</a> (DHGP) are also available in this assembly. Scaffolds that could not be unambiguously mapped to a chromosome arm have been concatenated into chrUn. chrUextra contains small scaffolds produced by the Celera shotgun assembler that could not be consistently joined with larger scaffolds. Because some of the chrUextra data are of low quality, researchers are encouraged to contact either BDGP or DHGP for further details on this resource. For more information on this assembly, see the Release 5 <a href="http://www.fruitfly.org/sequence/README.RELEASE5" target="_blank">assembly release notes</a>.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/dm3/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#fruitfly">Downloads</a> page. We'd like to +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/dm3/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#fruitfly">Downloads</a> page. We'd like to thank the BDGP, DHGP, and Flybase for providing data for this release. The dm3 Genome Browser was produced by Angie Hinrichs, Archana Thakkapallayil, Kayla Smith, and Donna Karolchik. The <em>D. melanogaster</em> browser annotations were generated by FlyBase, DHGP, and the UCSC Genome Bioinformatics group. See the <a href="credits.html#dm_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="062607"></a> <h2>Jun. 26, 2007 New 28-Species Conservation track released</h2> <p> We are pleased to announce the release of new versions of the Conservation and Most Conserved annotation tracks for the Human March 2006 Genome Browser (hg18, NCBI Build 36). The new Conservation track displays multiple alignments of 27 vertebrate species aligned to the human genome, along with measurements of evolutionary conservation across all species in the alignment and a separate measurement of conservation across the placental mammal subset of species in the alignment.</p> @@ -18056,33 +18056,33 @@ genomes in the track are available from our downloads server.</p> <p> In addition to the expanded species list, the new Conservation track features the following improvements: <ul> <li> additional filtering of pairwise alignments for each species to reduce paralogous alignments</li> <li> information about the quality of aligning species sequence included in the multiple alignment downloads</li> <li> new track configuration buttons to assist in selecting which species to display</li> </ul> <p> Bulk data downloads are available from the Genome Browser FTP server -(<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/multiz28way">alignments</a>, -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/phastCons28way">conservation</a>) or from the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#human">Downloads page</a>.</p> +(<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/multiz28way">alignments</a>, +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/phastCons28way">conservation</a>) or from the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#human">Downloads page</a>.</p> <p> The previous 17-vertebrate versions of the Conservation and Most Conserved tracks remain available on the hg18 Genome Browser as the "17-Way Cons" and "17-Way Most Cons" tracks.</p> <a name="061307"></a> <h2>Jun. 13, 2007 ENCODE findings released to public</h2> <p> The findings of the ENCODE project have been released to the public today, the culmination of a four-year effort to catalog the biologically functional elements in 1 percent of the human genome. The publications, which include a group paper in the 14 June 2007 issue of <a href="http://www.nature.com/nature/journal/v447/n7146/full/nature05874.html" target="_blank"><em>Nature</em></a> and 28 companion papers in the June 2007 issue of <a href="http://www.genome.org/content/vol17/issue6/" target="_blank"><em>Genome Research</em></a>, were authored by researchers from academic, governmental, and industry organizations located in 11 @@ -18113,51 +18113,51 @@ release</a> on the UCSC Center for Biomolecular Science and Engineering website.</p> <a name="052507"></a> <h2>May 25, 2007 Platypus Assembly available</h2> <p> We have released a Genome Browser and Blat server for the Jan. 2007 v5.0.1 draft assembly of <em>Ornithorhynchus anatinus</em> (UCSC version ornAna1) produced by the <a href="http://genome.wustl.edu/genome.cgi?GENOME=Ornithorhynchus%20anatinus" target="_blank">Genome Sequencing Center at Washington University</a>, St. Louis, MO (WUSTL).</p> <p> This assembly, which was sequenced using a combination of whole genome shotgun plasmid, fosmid and BAC end sequences, has a coverage of approximately 6X. It is comprised of about 1.84 Gb of actual sequence (excluding gap estimates), with 437 Mb anchored and ordered on chromosomes.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/ornAna1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#platypus">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/ornAna1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#platypus">Downloads</a> page. These data have <a href="credits.html#platypus_use">specific conditions for use</a>.</p> <p> We'd like to thank WUSTL for providing this assembly. The platypus Genome Browser was produced by Angie Hinrichs, Kayla Smith, Robert Kuhn, Brian Raney, and Donna Karolchik. The platypus browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="credits.html#platypus_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="051707"></a> <h2>May 17, 2007 Lizard Assembly available in Genome Browser</h2> <p> A Genome Browser and Blat server are now available for the Feb. 2007 v1.0 draft assembly (UCSC version anoCar1) of <em>Anolis carolinensis</em> produced by the <a href="http://www.broad.mit.edu/" target="_blank">Broad Institute</a>. This assembly has been sequenced to 6.8X coverage. The draft sequence contains 7,233 scaffolds comprised of nearly 1.74 Gb.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/anoCar1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#lizard">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/anoCar1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#lizard">Downloads</a> page. These data have <a href="credits.html#lizard_use">specific conditions for use</a>.</p> <p> We'd like to thank the Broad Institute for providing this assembly. The lizard Genome Browser was produced by Hiram Clawson, Archana Thakkapallayil, Robert Kuhn, and Donna Karolchik. The lizard browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="credits.html#lizard_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="051607"></a> <h2>May 16, 2007 New dates for OpenHelix seminars in L.A., D.C., Phila.</h2> <p> The dates for the upcoming OpenHelix Genome Browser seminars in Washington, D.C. and Los Angeles, CA have been changed. The following updated announcement includes the new dates:</p> <p> The UCSC Bioinformatics Group announces three regional seminars and hands-on computer workshops on @@ -18191,57 +18191,57 @@ <h2>May 14, 2007 Horse Genome Browser now available</h2> <p> The Jan. 2007 EquCab1 release of the horse genome (<em>Equus caballus</em>) is now available in the UCSC Genome Browser. This assembly, UCSC version equCab1, was produced by the <a href="http://www.broad.mit.edu/" target="_blank">Broad Institute</a>.</p> <p> The horse draft genome has been sequenced to 6.8X coverage. Approximately 84% of the sequence has been anchored to chromosomes, which include autosomes 1-31 and sex chromosome X. Unanchored contigs that could not be localized to a chromosome have been concatenated into the virtual chromosome "chrUn", separated by gaps of 1,000 bp. The mitochondrial sequence is also available in the Genome Browser as the virtual chromosome "chrM". For more details about the assembly, see the Broad Institute <a href="http://www.broad.mit.edu/mammals/horse/" target="_blank">Horse Genome Project</a> page.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/equCab1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#horse">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/equCab1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#horse">Downloads</a> page. These data have <a href="credits.html#horse_use">specific conditions for use</a>.</p> <p> The UCSC Horse Genome Browser was produced by Fan Hsu, Brooke Rhead, Robert Kuhn, Hiram Clawson, Angie Hinrichs, Kate Rosenbloom, and Donna Karolchik. See the <a href="credits.html#horse_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="042707"></a> <h2>Apr. 27, 2007 Medaka Genome Browser released</h2> <p> We're happy to announce the release of a Genome Browser and Blat server for the Medaka Version 1.0 draft assembly (Apr. 2006, UCSC version oryLat1). This assembly was produced in Japan by the <a href="http://www.nig.ac.jp/english/index.html" target="_blank">National Institute of Genetics</a> (NIG) and the <a href="http://medaka.utgenome.org/" target="_blank">University of Tokyo</a>. It is equivalent to Ensembl's Oct. 2005 MEDAKA1 data set.</p> <p> The v1.0 assembly has been sequenced to 10.6X coverage. It consists of approximately 700.4 million bp (excluding gaps) on chromosomes 1-24. 7,299 scaffolds comprised of nearly 36,500 contigs of unplaced sequence are displayed on the virtual chromosome "chrUn" These contigs are spaced with a 10 bp gap; scaffold gaps are 100 bp in size. The medaka mitochondrial sequence is also available in the Genome Browser as the virtual chromosome "chrM".</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/oryLat1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#medaka">Downloads</a> page. See the +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/oryLat1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#medaka">Downloads</a> page. See the University of Tokyo Medaka website for the <a href="http://medaka.utgenome.org/#policy" target="_blank">data release policy</a> for this assembly.</p> <p> The Medaka browser annotation tracks were generated by UCSC and collaborators worldwide. See the Genome Browser <a href="credits.html#medaka_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="041807"></a> <h2>Apr. 18, 2007 Free Genome Browser seminar at Experimental Biology 2007</h2> <p> OpenHelix will present a free introductory seminar on the Genome Browser during Experimental Biology 2007, April 29-May 1, in Washington, D.C. The tutorial will cover the topics needed to effectively use the Genome Browser, including: basic functionality of Genome Browser searching and BLAT use, Table Browser use, creating and using Custom Tracks, and an introduction to the Gene Sorter.</p> @@ -18262,32 +18262,32 @@ <h2>Apr. 11, 2007 Latest Fugu assembly available in Genome Browser</h2> <p> The UCSC Genome Browser now includes the latest release of the Fugu genome. The v4.0 whole genome shotgun assembly (Oct. 2004, UCSC fr2) was provided by the US DOE Joint Genome Institute (JGI) as part of the International Fugu Genome Consortium led by the JGI and the Singapore Institute of Molecular and Cell Biology (IMCB).</p> <p> This version has been sequenced to approximately 8.5X coverage. The assembly contains 7,213 scaffolds covering 393,312,790 bp. The UCSC browser displays the scaffolds on the virtual chromosome <em>chrUn</em> with gaps of 1,000 bp between scaffolds. The scaffolds range in size from 2,223 bp to 7,245,445 bp. Fifty percent of the sequence (196,648,171 bp) is contained within 125 scaffolds of size 858,115 or greater (N50). The Fugu mitochondrial sequence is also available as the virtual chromosome <em>chrM</em> (GenBank accession: NC_004299.1).</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/fr2/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#fugu">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/fr2/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#fugu">Downloads</a> page. These data have been freely provided by the JGI for use in the UCSC Genome Browser.</p> <p> Many thanks to the JGI, IMCB, and the International Fugu Genome Consortium for the assembly data. The UCSC Fugu Genome Browser was produced by Cory McClean, Hiram Clawson, Ann Zweig, and Donna Karolchik. The annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="credits.html#fugu_credits" target="_blank">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="040607"></a> <h2>Apr. 6, 2007 New UCSC Gene Prediction set released</h2> <p> We are pleased to announce the release of a new gene prediction set, UCSC Genes, on the latest human Genome Browser (hg18, NCBI Build 36). This annotation, which includes putative non-coding genes as well as protein-coding genes and 99.9% of RefSeq genes, is the next generation of the Known Genes set that UCSC has been providing for several years and supersedes the existing Known Genes @@ -18349,32 +18349,32 @@ <a name="032707"></a> <h2>Mar. 27, 2007 Stickleback assembly released in Genome Browser</h2> <p> We have released a Genome Browser and Blat server for the Feb. 2006 v1.0 draft assembly of <em>Gasterosteus aculeatus</em> produced by the <a href="http://www.broad.mit.edu/" target="_blank">Broad Institute</a>.</p> <p> This assembly has been sequenced to approximately 6X coverage. An estimated 87% of the sequence has been anchored to chromosomes (chrI - chrXXI). Of the remaining unanchored scaffolds, those that could be localized to a chromosome have been concatenated into the virtual chromosome "chrUn" with 1000bp gaps between scaffolds. The stickleback mitochondrial sequence is also available as the virtual chromosome "chrM".</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/gasAcu1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#stickleback">Downloads</a> page.These data +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/gasAcu1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#stickleback">Downloads</a> page.These data have <a href="credits.html#stickleback_use">specific conditions for use</a>.</p> <p> The stickleback browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="credits.html#stickleback_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="021607"></a> <h2>Feb. 16, 2007 New browser session-sharing function available</h2> <p> We are pleased to announce the release of a new session management functionality in the Genome Browser, which allows users to save and share browser sessions.</p> <p> Users are now able to configure their browsers with specific track combinations, including custom tracks, and save the configuraton options. Multiple sessions may be saved for future reference, for comparison of scenarios or for sharing with colleagues. Saved sessions persist for one year after @@ -18423,32 +18423,32 @@ <a name="012207"></a> <h2>Jan. 22, 2007 Cat assembly available in Genome Browser</h2> <p> The Mar. 2006 release of <em>Felis catus</em> (UCSC version felCat3) is now available in the Genome Browser. This assembly was produced by <a href="http://www.broad.mit.edu/" target="_blank">The Broad Institute</a> of MIT/Harvard and <a href="http://www.agencourt.com/" target="_blank">Agencourt Bioscience</a>.</p> <p> The felCat3 genome has been sequenced to 2X coverage and consists of 217,790 scaffolds. The total contig length for this assembly is approximately 1.6 Gb spanning nearly 4.0 Gb (with 60.1% in gaps). There are 749,376 contigs, with an N50 length of 2,506 bases. There are 149,283 supercontigs, with an N50 length of 49,769 bases (not including gaps). The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.</p> <p> The felCat3 sequence and annotation data can be downloaded from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/felCat3/"> FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#cat">Downloads</a> page. Please review the +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/felCat3/"> FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#cat">Downloads</a> page. Please review the <a href="/goldenPath/credits.html#cat_use">guidelines</a> for using the cat assembly data.</p> <p> Many thanks to The Broad Institute for providing these data. The UCSC cat Genome Browser was produced by Heather Trumbower, Angie Hinrichs, Mark Diekhans, Brooke Rhead, and Archana Thakkapallayil. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the Genome Browser <a href="/goldenPath/credits.html#cat_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to the release of this browser.</p> <a name="010107"></a> <h2>Jan. 1, 2007 Upcoming Genome Browser seminars: SF, Seattle, NYC, Cleveland</h2> <p> The UCSC Bioinformatics Group announces four regional seminars and hands-on computer workshops on the UCSC Genome Browser, presented by <a href="http://www.openhelix.com/" target="_blank">OpenHelix:</a></p> @@ -18540,49 +18540,49 @@ Create and upload description pages for custom tracks</li> <li> Custom tracks will now persist on our server for 48 hours after last access (rather than 8 hours)</li> </ul> <p> For more information about the new custom tracks functionality, see the Genome Browser <a href="help/customTrack.html">Users's Guide</a>. The hgCustom CGI was written by Kate Rosenbloom with the assistance of Archana Thakkapallayil, Ann Zweig and other members of the UCSC Genome Bioinformatics Group.</p> <a name="090706"></a> <h2>Sep. 7, 2006 Old Rhesus assembly archived</h2> <p> The Jan. 2005 rheMac1 draft assembly has been archived. The data remain available on our -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/rheMac1/">downloads server</a>, but blat +<a href="http://hgdownload.gi.ucsc.edu/goldenPath/rheMac1/">downloads server</a>, but blat services are no longer supported. </p> <a name="080806"></a> <h2>Aug. 8, 2006 New Opossum assembly available in Genome Browser</h2> <p> The UCSC Genome Browser now includes the latest draft assembly of the opossum genome. The Jan. 2006 release of <em>Monodelphis domestica</em> (UCSC version monDom4) was sequenced and assembled by <a href="http://www.broad.mit.edu/mammals/opossum/" target="_blank">The Broad Institute</a>, Cambridge, MA, USA.</p> <p> This draft, which has approximately 6.5X coverage, has an assembly length of nearly 3.61 billion bp including gaps (3.50 billion bp without gaps) contained on chromosomes 1-8, X, and Un. The N50 of the genome including gaps is 104,359 bp; the N50 without gaps is 107,990. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.</p> <p> The monDom4 sequence and annotation data can be downloaded from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/monDom4/"> FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/monDom4/">Downloads</a> page. Please review the +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/monDom4/"> FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/goldenPath/monDom4/">Downloads</a> page. Please review the <a href="credits.html#opossum_use">guidelines</a> for using the opposum assembly data.</p> <p> Many thanks to The Broad Institute for providing these data. The UCSC opossum Genome Browser was produced by Hiram Clawson, Archana Thakkapallayil, Ann Zweig, Kayla Smith and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the Genome Browser <a href="credits.html#opossum_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to the release of this browser.</p> <a name="080106"></a> <h2>Aug. 1, 2006 v2.1 Chicken assembly available in Genome Browser</h2> <p> We have updated the Chicken Genome Browser to include the May 2006 v2.1 assembly (UCSC version galGal3) produced by the Genome Sequencing Center at the Washington University School of Medicine in St. Louis, MO, USA (WUSTL). The source of this sequence was a female inbred Red Jungle Fowl (<em>Gallus gallus</em>), the ancestor of domestic chickens. The chicken genome is the first of the @@ -18596,32 +18596,32 @@ the virtual chromosomes "chr*_random", separated by gaps of 10,000 bp. Unanchored contigs that could not be localized to a chromosome have been concatenated into the virtual chromosome "chrUn_random", separated by gaps of 100 bp to reduce the total size of chrUn_random. The chicken mitochondrial sequence is also available as the virtual chromosome "chrM".</p> <p> Although centromere positions are indicated on this assembly, little is known of their exact sequence. The centromeres of 18 chromosomes were tentatively localized based on FISH hybridization using BAC clones, genetic markers flanking the centromeres in coordination with mapping gaps in the physical map, repetitive sequence content, and analysis of proximity to the constrictions of the mitotic metaphase chromosomes. For more information on the process used to create the chromosomal sequences and assign centromere locations, see the WUSTL <a href="http://genome.wustl.edu/genomes/detail/gallus-gallus/" target="_blank">Gallus gallus genome</a> page.</p> <p> Bulk downloads of the chicken sequence and annotations may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/galGal3/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#chicken">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/galGal3/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#chicken">Downloads</a> page. These data have <a href="credits.html#chicken_use">specific conditions for use</a>.</p> <p> We'd like to thank WUSTL, who provided the sequence, physical map, assembly, and assembly/map for this release. The genetic mapping and linkage analysis were produced through a collaborative effort of labs in The Chicken Mapping Consortium. The chicken browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="credits.html#chicken_credits">Credits</a> page for a detailed list of acknowledgements. The UCSC Chicken Genome Browser was produced by Angie Hinrichs, Kayla Smith, and Donna Karolchik.</p> <a name="072006"></a> <h2>Jul. 20, 2006 New Chimpanzee Genome Browser released</h2> <p> We are happy to announce the release of a Genome Browser for the latest release of the chimpanzee (Pan troglodytes) genome. The Mar. 2006 assembly -- labeled Chimp Build 2 Version 1 (UCSC version panTro2) -- was produced by the @@ -18647,149 +18647,149 @@ of 9.7 Mb. The total contig length, not including estimated gap sizes, is 2.97 Gb. Of that total, 2.82 Gb of sequence have been ordered and oriented along specific chimpanzee chromosomes, 107 Mb have been placed in chr*_random, and 50 Mb remain in chrUn.</p> <p> A major difference between this assembly and the previous Nov. 2003 version is the chromosomal numbering scheme, which has been changed to reflect a new standard that preserves orthology with human chromomes. Proposed by <a href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=15218271&query_hl=1&itool=pubmed_docsum" target="_blank">E.H. McConkey</a> in 2004, the new numbering convention was subsequently endorsed by the International Chimpanzee Sequencing and Analysis Consortium. This standard assigns the identifiers "2a" and "2b" to the two chimp chromosomes that fused in the human genome to form chromosome 2. Note that the genome assembly shown in the Nov. 2003 panTro1 Genome Browser retains the older numbering scheme, in which these chromosomes are numbered 12 and 13.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/panTro2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#chimp">Downloads</a> page. The complete set +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/panTro2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#chimp">Downloads</a> page. The complete set of sequence reads is available at the <a href="https://www.ncbi.nlm.nih.gov/Traces" target="_blank">NCBI trace archive</a>. These data have <a href="credits.html#chimp_use">specific conditions for use</a>.</p> <p> We'd like to thank the International Chimpanzee Sequencing and Analysis Consortium, Washington University at St. Louis School of Medicine Genome Sequencing Center, and the Broad Institute for providing this sequence. We'd also like to acknowledge the UCSC team who worked on this release: Kate Rosenbloom, Brian Raney, Hiram Clawson, Ann Zweig, Archana Thakkapallayil, and Donna Karolchik. The chimpanzee browser annotation tracks were generated by UCSC and collaborators worldwide.</p> <a name="062006"></a> <h2>Jun. 20, 2006 Genome Browser released for Baylor v3.4 Rat assembly</h2> <p> The UCSC Genome Bioinformatics group has released a Genome Browser for the v3.4 rat (<em>Rattus norvegicus</em>) genome. This assembly--UCSC version rn4, November 2004--was produced by the Atlas group at <a href="http://www.hgsc.bcm.edu/" target="_blank">Baylor Human Genome Sequencing Center</a> (HGSC) as part of the Rat Genome Sequencing Consortium.</p> <p> The sequence was assembled using a hybrid approach that combines the clone-by-clone and whole genome shotgun methods. The assembly is a minor update to version 3.3 that spliced in 54.6 Mb finished BAC sequences; the overall statistics are unchanged from releases 3.0 to 3.4.</p> <p> The 3.x assemblies reflect several sequence additions and software improvements over the previous 2.x assemblies, including the sequencing of over 1100 new BACs to cover gaps, an improved marker set from the Medical College of Wisconsin, a new FPC map from the BC Cancer Agency Genome Sciences Centre, and improved linking of bactigs. For detailed information and statistics about the 3.x assemblies, see the Baylor HGSC <a href="http://www.hgsc.bcm.tmc.edu/projects/rat/" target="_blank">Rat Genome Project</a> web page. </p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/rn4/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#rat">Downloads</a> page. These data are made +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/rn4/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#rat">Downloads</a> page. These data are made available with <a href="/goldenPath/credits.html#rat_use">specific conditions for use</a>. <p> We'd like to thank the Rat Genome Sequencing Consortium and the Baylor HGSC for providing this assembly. We'd also like to acknowledge the UCSC team who produced the rn4 Genome Browser: Angie Hinrichs, Fan Hsu, Brooke Rhead, Archana Thakkapallayil, Kayla Smith, Ann Zweig, Robert Kuhn, and Donna Karolchik. The rn4 annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="credits.html#rat_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="061206"></a> <h2>Jun. 12, 2006 Latest <em>X. tropicalis</em> assembly available in Browser</h2> <p> The v.4.1 <em>Xenopus tropicalis</em> assembly is now available on the UCSC Genome Browser. This whole genome shotgun assembly (xenTro2, Aug. 2005) was generated by the U.S. DOE Joint Genome Institute (JGI) using the Jazz assembler. It contains 19,501 scaffolds with an average coverage of 7.65X. Roughly half the genome is contained in 272 scaffolds, each of at least 1.56 Mb in length.</p> <p> In this release, some scaffolds showing homology to a known prokaryotic contaminant as well as non-cellular or vector contamination have been removed by the JGI and placed in a separate directory. The <em>X. tropicalis</em> assembly will be improved over the coming year by additional sequencing of large insert clones, targeted gap closure, and the incorporation of physical and genetic mapping information as it becomes available.</p> <p> For more information about the 4.1 assembly, see the JGI <a href="http://genome.jgi-psf.org/Xentr4/Xentr4.home.html" target="_blank"><em>X. tropicalis</em> website</a>.</p> <p> The xenTro2 sequence and annotation data can be downloaded from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/xenTro2/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#xenTro">downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/xenTro2/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#xenTro">downloads</a> page. These data have <a href="http://genome.jgi-psf.org/Xentr4/Xentr4.download.html" target="_blank">specific conditions for use</a>.</p> <p> Many thanks to the JGI and the other institutions who contributed to the sequencing and mapping effort for this release. The xenTro2 Genome Browser was produced by Angie Hinrichs, Kayla Smith, Robert Kuhn, and Donna Karolchik. The xenTro2 annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="credits.html#xenTro_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="052506"></a> <h2>May 25, 2006 - Zv6 Zebrafish Browser Released</h2> <p> The latest zebrafish assembly -- Zv6 (UCSC version danRer4, March 2006) -- is now available in the UCSC Genome Browser. The Zv6 assembly was produced by The Wellcome Trust Sanger Institute in collaboration with the Max Planck Institute for Developmental Biology in Tuebingen, Germany, and the Netherlands Institute for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands.</p> <p> This assembly consists of 1,626,077,335 bp in 6.653 scaffolds (N50 = 1,247,221 bp) with a sequence coverage of approximately 6.5-7x. The sequence has been anchored to chromosomes 1-25, chrM (mitochondrial), chrNA_random, and chrUn_random. For more information about this assembly, see the Sanger Institute web page for the <a href="http://www.sanger.ac.uk/Projects/D_rerio/Zv6_assembly_information.shtml/" target="_blank"><em>Danio rerio</em> Sequencing Project</a>.</p> <p> The danRer4 sequence and annotation data can be downloaded from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/danRer4/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#zebrafish">downloads</a> page. Please review +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/danRer4/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#zebrafish">downloads</a> page. Please review the <a href="http://www.sanger.ac.uk/Projects/use-policy.shtml" target="_blank">guidelines</a> for using these data.</p> <p> We'd like to thank the Wellcome Trust Sanger Institute, the Max Planck Institute for Developmental Biology, Hubrecht Laboratory and the other institutions who contributed to the sequencing and mapping effort of this release. Special thanks to the Zebrafish Genome Initiative at Children's Hospital in Boston for their collaboration on this release. The UCSC zebrafish Genome Browser was produced by Rachel Harte, Archana Thakkapallayil, Robert Kuhn, Ann Zweig, and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the <a href="credits.html#zebrafish_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to the release of this browser.</p> <a name="051006"></a> <h2>May 10, 2006 NCBI Mouse Build 36 released in Genome Browser</h2> <p> The latest mouse genome assembly from the Mouse Genome Sequencing Consortium, NCBI Build 36, is now available in the UCSC Genome Browser. This version (UCSC version mm8) is considered to be essentially finished.</p> <p> The Build 36 assembly includes approximately 2.6 Gb of sequence on chromosomes 1-19, X, Y, M (mitochondrial DNA) and Un (unmapped clone contigs). For in-depth information about the process used to assemble this version, see the NCBI website. On chromosome Y in this assembly, only the short arm has reliable mapping data; therefore, most of the contigs on the Y chromosome are unplaced. Note that the UCSC mm8 database contains only the reference strain C57BL/6J.</p> <p> The mm8 sequence and annotation data may be downloaded from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/mm8/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/mm8/">Downloads</a> web page. The mm8 annotation +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/mm8/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/goldenPath/mm8/">Downloads</a> web page. The mm8 annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> We'd like to thank Deanna Church and the Mouse Genome Sequencing Consortium for this assembly. We'd also like to acknowledge the work of the UCSC mm8 team: Hiram Clawson, Fan Hsu, Kayla Smith, Ann Zweig, Robert Kuhn, Brooke Rhead, Archana Thakkapallayil, and Donna Karolchik. For a complete list of the individuals and organizations who participated in this assembly, see the <a href="credits.html#mouse_credits">Credits</a> page.</p> <a name="041406"></a> <h2>Apr. 14, 2006 NCBI Build 36.1 human reference sequence available in browser</h2> <p> The latest human genome reference sequence assembly (NCBI Build 36.1, March 2006) is now available as database hg18 in the UCSC Genome Browser. This sequence, which was obtained from NCBI, was produced by the International Human Genome Sequencing Consortium.</p> <p> @@ -18811,32 +18811,32 @@ </ul> <p> See the <a href="http://www.sanger.ac.uk/HGP/Chr6/MHC/" target="_blank">Wellcome Trust Sanger Institute MHC Haplotype Project</a> web site for additional information on the chr6 alternate haplotype assemblies.</p> <p> The Y chromosome in this assembly contains two pseudoautosomal regions (PARs) at chrY:1-2709520 and chrY:57443438-57772954. These sequences were taken from the corresponding regions in the X chromosome and are exact duplications of the X chromosome sequences.</p> <p> For further information on NCBI Build 36.1, see the NCBI <a href="https://www.ncbi.nlm.nih.gov/mapview/stats/BuildStats.cgi?taxid=9606&build=36&ver=1" target="_blank">Build 36.1 release notes</a>.</p> <p> Bulk downloads of the data are available from the UCSC downloads server via -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18" target="_blank">ftp</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#human" target="_blank">http</a>. We recommend +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18" target="_blank">ftp</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#human" target="_blank">http</a>. We recommend that you use ftp or rsync for downloading large or multiple files.</p> <p> We'd like to thank NCBI and the International Human Genome Sequencing Consortium for furnishing the data, and the entire UCSC Genome Browser staff for contributing to this release. Fan Hsu led the UCSC engineering effort; QA was headed up by Ann Zweig.</p> <a name="030606"></a> <h2>Mar. 6, 2006 Purple Sea Urchin genome assembly available in Genome Browser</h2> <p> The Apr. 2005 release of the Purple Sea Urchin genome (<em>Strongylocentrotus purpuratus</em>) is now available in the UCSC Genome Browser. This assembly, UCSC version strPur1, was produced by the Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC) and corresponds to their Spur_0.5 whole genome shotgun assembly.</p> <p> This release was assembled from whole genome shotgun reads using the Atlas genome assembly system @@ -18847,32 +18847,32 @@ from this assembly and will be placed in a subsequent version of the draft sequence.</p> <p> This is a draft sequence and may contain errors; therefore, users should exercise caution. Typical errors in draft genome sequences include misassemblies of repeated sequences, collapses of repeated regions, and unmerged overlaps (<em>e.g.</em> due to polymorphisms) creating artificial duplications. However, base accuracy in contigs (contiguous blocks of sequence) is usually very high with most errors near the ends of contigs.</p> <p> More assembly details can be found in the <a href="ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Spurpuratus/fasta/Spur20050415/READMEApril2005.txt" target="_blank">Spur_0.5 README file</a> and on the BCM HGSC <a href="http://www.hgsc.bcm.tmc.edu/projects/seaurchin/" target="_blank">Sea Urchin Genome Project</a> web page.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/strPur1">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#urchin">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/strPur1">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#urchin">Downloads</a> page. These data have <a href="http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html" target="_blank">specific conditions for use</a>. The strPur1 annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="credits.html#urchin_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="022706"></a> <h2>Feb. 27, 2006 Upcoming Genome Browser seminars in Texas, Florida and Washington, DC</h2> <p> The UCSC Bioinformatics Group announces four regional seminars and hands-on computer workshops on the UCSC Genome Browser, presented by <a href="http://www.openhelix.com/" target="_blank">OpenHelix:</a></p> <ul> <li> Houston, TX -- Tuesday, Mar. 14</li> @@ -18906,32 +18906,32 @@ The latest zebrafish assembly -- Zv5 (UCSC version danRer3, May 2005) -- is now available in the UCSC Genome Browser and Blat server. The Zv5 assembly was produced by The Wellcome Trust Sanger Institute in collaboration with the Max Planck Institute for Developmental Biology in Tuebingen, Germany, and the Netherlands Institute for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands.</p> <p> This assembly consists of 1,630,306,866 bp in 16,214 scaffolds (N50 = 1,116,981 bp) with a sequence coverage of approximately 6.5-7x. The assembly has been tied to the fingerprint contig map (data freeze 15th February, 2005) and contains 699 Mb from 4,519 sequenced clones.</p> <p> For more information about this assembly, see the Sanger Institute web page for the <a href="http://www.sanger.ac.uk/Projects/D_rerio/" target="_blank"><em>Danio rerio</em> Sequencing Project</a>.</p> <p> The danRer3 sequence and annotation data can be downloaded from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/danRer3/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#zebrafish">downloads</a> page. Please review +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/danRer3/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#zebrafish">downloads</a> page. Please review the <a href="http://www.sanger.ac.uk/Projects/use-policy.shtml" target="_blank">guidelines</a> for using these data.</p> <p> We'd like to thank the Wellcome Trust Sanger Institute, the Max Planck Institute for Developmental Biology, Hubrecht Laboratory and the other institutions who contributed to the sequencing and mapping effort of this release. Special thanks to the Zebrafish Genome Initiative at Children's Hospital in Boston for their collaboration on this release. The UCSC zebrafish Genome Browser was produced by Rachel Harte, Jennifer Jackson, Ann Zweig, Ali Sultan-Qurraie, and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the <a href="credits.html#zebrafish_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to the release of this browser.</p> <a name="020906"></a> <h2>Feb. 9, 2006 New Rhesus Macaque Browser released</h2> <p> @@ -18945,149 +18945,149 @@ to have its genome sequenced. Overall, the rhesus genome shares approximately 92 to 95 precent of its sequence with the human, compared with the chimp at 98 precent. Because of its genetic, physiologic, and metabolic similarities to the human and chimp, the rhesus is an ideal reference point for comparisons among the three primates.</p> <p> The groups in the Macaque Genome Sequencing Consortium produced preliminary assemblies of the genome data using different and complementary approaches. The resulting data were combined into a single, high-density "melded" assembly by a team at J. Craig Venter Institute. This collaboration made use of published rhesus maps, the BAC fingerprint map from the Michael Smith Genome Sciences Centre, and the human reference genome sequence. The v.1.0 assembly covers about 93 percent of the rhesus genome. For more information about the rheMac2 assembly, see the Baylor <a href="http://www.hgsc.bcm.tmc.edu/projects/rmacaque/" target="_blank">Rhesus Monkey Project</a> web page.</p> <p> The rheMac2 sequence and annotation data can be downloaded from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/rheMac2/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#rhesus">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/rheMac2/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#rhesus">Downloads</a> page. These data have specific <a href="http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html" target="_blank">conditions for use</a>.</p> <p> Many thanks to Baylor College of Medicine, the Macaque Genome Sequencing Consortium, and the other institutions who contributed to the sequencing and mapping effort of the v.1.0 release. The UCSC Rhesus Genome Browser was produced by Robert Baertsch, Kayla Smith, Ann Zweig, Robert Kuhn, and Donna Karolchik. The initial set of rheMac2 annotation tracks was generated by the <a href="../staff.html">UCSC Genome Bioinformatics Group</a>. See the <a href="credits.html#rhesus_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to the release of this browser.</p> <a name="011806"></a> <h2>Jan. 18, 2006 <em>D. sechellia</em> Browser released</h2> <p> The Oct. 2005 <em>D. sechellia</em> assembly (UCSC version droSec1) is now available in the UCSC Genome Browser. This version was sequenced and assembled by the Broad Institute of MIT and Harvard.</p> <p> Downloads of the droSec1 data and annotations can be obtained from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/droSec1/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#droSec">Downloads</a> page. The initial set +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/droSec1/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#droSec">Downloads</a> page. The initial set of droSec1 annotation tracks were generated by UCSC.</p> <p> Many thanks to the Broad Institute for providing the sequence and assembly of this genome. The UCSC <em>D. sechellia</em> Genome Browser was produced by Angie Hinrichs, Kayla Smith and Donna Karolchik. See the <a href="credits.html#droSec_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="011106"></a> <h2>Jan. 11, 2006 <em>D. yakuba</em> Browser update</h2> <p> The latest <em>D. yakuba</em> assembly is now available in the UCSC Genome Browser. This version — Release 2.0, dated Nov. 2005 (UCSC version droYak2) — was sequenced and assembled by the Genome Sequencing Center, Washington University (WUSTL) School of Medicine in St. Louis. </p> <p> The whole genome shotgun (WGS) assembly includes both raw shotgun data and data from two rounds of automated, directed read selection, which has improved the sequence quality and narrowed or (in some instances) closed gaps. For more assembly information and statistics, see the WUSTL Genome Sequencing Center <a href="http://genome.wustl.edu/genome.cgi?GENOME=Drosophila%20yakuba&GROUP=6" target="_blank"><em>Drosophila yakuba</em></a> web page.</p> <p> Downloads of the droYak2 data and annotations can be obtained from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/droYak2/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#droYak">Downloads</a> page. The initial set +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/droYak2/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#droYak">Downloads</a> page. The initial set of droYak2 annotation tracks was generated by UCSC.</p> <p> Thanks to the Genome Sequencing Center at WUSTL School of Medicine for providing the sequence and assembly of this genome. The droYak2 Genome Browser was produced by Angie Hinrichs, Jennifer Jackson and Donna Karolchik. See the <a href="credits.html#droYak_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="010406"></a> <h2>Jan. 4, 2006 <em>D. persimilis</em> Genome Browser released</h2> <p> The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the <em>D. persimilis</em> genome. The Oct. 2005 release (UCSC version droPer1) was sequenced and assembled by the Broad Institute of MIT and Harvard. The <em>D. persimilis</em> assembly joins nine other Drosophila species featured in the UCSC Genome Browser.</p> <p> Downloads of the droPer1 data and annotations can be obtained from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/droPer1/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#droPer">Downloads</a> page. The droPer1 +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/droPer1/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#droPer">Downloads</a> page. The droPer1 annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> Thanks to the Broad Institute for providing the sequence and assembly of this genome. The UCSC <em>D. persimilis</em> Genome Browser was produced by Angie Hinrichs, Kayla Smith, Robert Kuhn, Jennifer Jackson and Donna Karolchik. See the <a href="credits.html#droPer_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <!---------------- 2005 archived news ---------------> <a name="2005"></a> <a name="122005"></a> <h2>Dec. 20, 2005 Dog Genome Browser update released</h2> <p> UCSC has updated the dog Genome Browser to include the May 2005 v2.0 assembly (UCSC version canFam2) sequenced and assembled by the Broad Institute of MIT and Harvard and Agencourt Bioscience. The whole genome shotgun sequence is based on 7.6X coverage of the dog genome which includes more than 98% of the euchromatic genome.</p> <p> The dog genome, which contains approximately 2.5 billion base pairs, is similar in size to the genomes of humans and other mammals. The boxer breed was selected for the initial sequencing effort, based on the lower variation rate in its genome relative to other breeds. In addition to the boxer, samples from several other dog breeds were used to generate a set of single nucleotide polymorphisms (SNPs) to facilitate disease studies. The SNPs are available from the Broad Institute <a href="http://www.broad.mit.edu/ftp/pub/papers/dog_genome/snps_canfam2/" target="_blank">dog SNP</a> web page. For more information about the dog draft assembly, see the Broad Institute <a href="http://www.broad.mit.edu/mammals/dog/" target="_blank">Dog Genome Sequencing Project</a> web page.</p> <p> The dog sequence and annotation data can be downloaded from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/canFam2/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#dog">downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/canFam2/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#dog">downloads</a> page. These data have <a href="credits.html#dog_use">specific conditions for use</a>.</p> <p> Many thanks to the Broad Institute of MIT and Harvard, Agencourt Bioscience, and the other institutions who contributed to the sequencing, assembly, and mapping efforts. The canFam2 Genome Browser team included Angie Hinrichs, Jennifer Jackson, and Donna Karolchik. See the <a href="credits.html#dog_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="121505"></a> <h2>Dec. 15, 2005 New Mouse assembly available in Genome Browser</h2> <p> The latest mouse genome assembly from the Mouse Genome Sequencing Consortium, NCBI Build 35 (UCSC version mm7), is now available in the UCSC Genome Browser.</p> <p> The Build 35 assembly includes approximately 2.6 Gb of sequence, of which about 2.2 Gb is finished sequence. Chromosomes 2, 4, 11 and X are finished in this build. To review in-depth statistics on the assembly, see the NCBI <a href="https://www.ncbi.nlm.nih.gov/genome/guide/mouse/release_notes.html" target="_blank">Build 35 Data</a> web page. Please note that the UCSC mm7 database contains only the reference strain C57BL/6J.</p> <p> The mm7 sequence and annotation data may be downloaded from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/mm7/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/mm7/">Downloads</a> web page. The mm7 annotation +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/mm7/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/goldenPath/mm7/">Downloads</a> web page. The mm7 annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> We'd like to thank Deanna Church and the Mouse Genome Sequencing Consortium for this assembly. We'd also like to acknowledge the work of the UCSC mm7 team: Hiram Clawson, Fan Hsu, Ann Zweig, Kayla Smith, Robert Kuhn and Donna Karolchik. For a complete list of the individuals and organizations who participated in this assembly, see the <a href="credits.html#mouse_credits">Credits</a> page.</p> <a name="1202b05"></a> <h2Dec. 2, 2005 Announcing the VisiGene Image Browser</h2> <p> We are pleased to announce the release of a new software tool in the Genome Browser collection, the <a href="../cgi-bin/hgVisiGene">VisiGene Image Browser</a>. VisiGene offers the ability to view <em>in situ</em> images, allowing examination of expression patterns at both the tissue and cellular levels. The browser serves as a virtual microscope that lets viewers retrieve images that meet specific search criteria, then interactively zoom and scroll across the collection. The VisiGene @@ -19153,55 +19153,55 @@ information, visit <a href="http://www.openhelix.com" target="_blank">www.openhelix.com</a> or call 1-888-861-5051.</p> <a name="101105"></a> <h2>Oct. 11, 2005 <em>D. grimshawi</em> Browser now available</h2> <p> The UCSC Genome Bioinformatics Group has added the <em>Drosophila grimshawi</em> genome to the collection of fly genomes available in the UCSC Genome Browser. This assembly (UCSC version droGri1, Aug. 2005) was produced by <a href ="http://www.agencourt.com/" target="_blank">Agencourt Bioscience Corporation</a> in Beverly, MA, USA, using the Arachne assembler.</p> <p> The droGri1 assembly contains 25,052 scaffolds ranging in size from 196 bases to 14,170,260 bases.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/droGri1/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#droGri">Downloads</a> page. Please review the data use guidelines outlined in the README.txt files that accompany the downloads. The data use +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/droGri1/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#droGri">Downloads</a> page. Please review the data use guidelines outlined in the README.txt files that accompany the downloads. The data use restrictions are also available on the Genome Browser <a href="credits.html#droGri_use">Credits</a> page.</p> <p> We'd like to thank Agencourt Bioscience Corporation for providing this assembly. The UCSC droGri1 browser was produced by Angie Hinrichs, Brian Raney, Jennifer Jackson, Kayla Smith and Donna Karolchik. The UCSC Genome Bioinformatics Group generated the initial set of annotation tracks. See the <a href="credits.html#droGri_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="100705"></a> <h2>Oct. 7, 2005 New <em>D. ananassae</em> Browser released</h2> <p> The UCSC Genome Bioinformatics Group has updated the <em>Drosophila ananassae</em> Genome Browser to the 1 August, 2005 assembly. This version (UCSC version droAna2) was produced by <a href="http://www.agencourt.com/" target="_blank">Agencourt Bioscience Corporation</a> using the <a href="http://www.broad.mit.edu/wga/" target="_blank">Arachne assembler</a>.</p> <p> The assembly contains 13,772 scaffolds ranging in size from 55 bases to 23,697,768 bases, with a mean size of 16822.3 and median of 1537.</p> <p> Sequence and annotation data for the droAna2 assembly can be downloaded from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/droAna2">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#droAna">downloads</a> page. Please review the +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/droAna2">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#droAna">downloads</a> page. Please review the data use guidelines outlined in the README.txt files that accompany the downloads. The data use restrictions are also available on the Genome Browser <a href="credits.html#droAna_credits">credits</a> page.</p> <p> We'd like to thank Agencourt Bioscience Corporation for this assembly. The UCSC droAna2 browser was produced by Angie Hinrichs, Brian Raney, Ann Zweig, Kayla Smith and Donna Karolchik. The UCSC Genome Bioinformatics Group generated the initial set of annotation tracks. See the <a href="credits.html#droAna_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="100405"></a> <h2>Oct. 4, 2005 Updated Cow Browser available</h2> <p> The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the Mar. 2005 Btau_2.0 draft assembly of the cow genome. This assembly (UCSC version bosTau2) was provided by @@ -19209,69 +19209,69 @@ <p> The Btau_2.0 release was assembled from whole genome shotgun (WGS) reads using the Atlas genome assembly system. Several WGS libraries, with inserts of 2 - 4 kb and 4 - 6 kb, were used to produce the data. Approximately 23 million reads were assembled, representing about 17.7 Gb of sequence and 6.2x coverage of the (clonable) bovine genome. Highly repeated sequences and BAC clones sequences were omitted from this assembly; these will be placed in a subsequent version of the draft sequence. The assembly contains chromosomes 1-29, X, M, and Bin0, as well as 98058 scaffolds. For details about changes UCSC made to the assembly format for display purposes, please see the bosTau2 Genome Browser <a href="../cgi-bin/hgGateway?db=bosTau2">gateway page</a>.</p> <p> More information on the Btau_2.0 assembly can be found on the Baylor <a href="http://www.hgsc.bcm.tmc.edu/projects/bovine/" target="_blank">Bovine Genome Project</a> web page.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/bosTau2/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#cow">Downloads</a> page. Please refer to the +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/bosTau2/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#cow">Downloads</a> page. Please refer to the Baylor <a href="http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html" target="_blank">conditions of use</a> regarding these data. The bosTau2 annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> We'd like to thank Baylor College of Medicine for the bovine sequence and assembly. We'd also like to acknowledge the members of the UCSC Genome Bioinformatics Group who contributed to the Cow Genome Browser: Galt Barber, Brian Raney, Mark Diekhans, Jennifer Jackson and Donna Karolchik. See the <a href="credits.html#cow_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="092005"></a> <h2>Sep. 20, 2005 Three Drosophila assemblies released in Genome Browser</h2> <p> The UCSC Genome Bioinformatics Group has added three more Drosophila genomes to the collection of fly genomes in the UCSC Genome Browser. The new genomes, which include the initial assembly of <em>D. erecta</em> (droEre1, Aug. 2005) and the updated assemblies of <em>D. virilis</em> (droVir2, Aug. 2005) and <em>D. mojavensis</em> (droMoj2, Aug. 2005), were produced by <a href ="http://www.agencourt.com/" target="_blank">Agencourt Bioscience Corporation</a> in Beverly, MA, USA. All three genomes were assembled using the Arachne assembler.</p> <p> The droEre1 assembly contains 5,124 scaffolds ranging in size from 154 bases to 26,647,023 bases, with a mean size of 29832.7 and median of 1740. The droVir2 assembly consists of 13,562 scaffolds ranging in size from 57 bases to 25,269,527 bases, with a mean size of 15263.1 and median of 1249. The droMoj2 assembly is comprised of 6,843 scaffolds ranging in size from 101 bases to 34,172,700 bases, with a mean size of 28389.6 and median of 1671.</p> <p> Bulk downloads of the sequence and annotation data are available from the UCSC downloads server:</p> <ul> <li> - droEre1 - <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/droEre1">FTP</a>, - <a href="http://hgdownload.soe.ucsc.edu/goldenPath/droEre1">HTTP</a></li> + droEre1 - <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/droEre1">FTP</a>, + <a href="http://hgdownload.gi.ucsc.edu/goldenPath/droEre1">HTTP</a></li> <li> - droVir2 - <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/droVir2">FTP</a>, - <a href="http://hgdownload.soe.ucsc.edu/goldenPath/droVir2">HTTP</a</li> + droVir2 - <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/droVir2">FTP</a>, + <a href="http://hgdownload.gi.ucsc.edu/goldenPath/droVir2">HTTP</a</li> <li> - droMoj2 - <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/droMoj2">FTP</a>, - <a href="http://hgdownload.soe.ucsc.edu/goldenPath/droMoj2">HTTP</a></li> + droMoj2 - <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/droMoj2">FTP</a>, + <a href="http://hgdownload.gi.ucsc.edu/goldenPath/droMoj2">HTTP</a></li> </ul> <p> Please review the data use guidelines outlined in the README.txt files that accompany the downloads. The data use restrictions are also available on the Genome Browser <a href="credits.html">credits</a> page.</p> <p> We'd like to thank Agencourt Bioscience Corporation for providing these assemblies. The UCSC Drosophila browsers were produced by Angie Hinrichs, Brian Raney, Jennifer Jackson and Donna Karolchik. The UCSC Genome Bioinformatics Group generated the initial set of annotation tracks. See the <a href="credits.html">credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="090905"></a> <h2>Sep. 9, 2005 <em>C. intestinalis</em> v2.0 Genome Browser released</h2> <p> @@ -19280,32 +19280,32 @@ <p> This whole genome shotgun assembly was constructed with the JGI assembler, JAZZ, using paired-end sequencing reads. Starting with a coverage of 11x, additional data -- including BAC and FISH markers -- were used to map scaffolds to chromosome arms. The size of this assembly, including unmapped scaffolds, is 173 Mb, with 94 Mb of the sequence mapped to chromosome arms.</p> <p> For more information about the ci2 assembly, see the JGI <a href="http://genome.jgi-psf.org/ciona4/ciona4.info.html" target="_blank"><em>C. intestinalis</em> project page</a>. Additional information and an analysis of the euchromatic regions of this genome may be found in Dehal, P. <em>et al.</em> <a href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12481130&query_hl=1" target="_blank">The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins</a>. <em>Science</em> <B>298</B>(5601), 2157-67 (2002).<p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/ci2/" target="_blank">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#ciona" target="_blank">Downloads page</a>. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/ci2/" target="_blank">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#ciona" target="_blank">Downloads page</a>. The ci2 annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="credits.html#ciona_credits">Credits page</a> for a detailed list of the organizations and individuals who contributed to this release.</p> <p> Many thanks to the JGI and their collaborators for providing the v2.0 sequence and annotations. The ci2 Genome Browser was produced by Brian Raney, Mark Diekhans, Ann Zweig, Kayla Smith, Robert Kuhn and Donna Karolchik.</p> <a name="081105"></a> <h2Aug. 11, 2005 Upcoming Genome Browser seminars - San Francisco, Seattle, Chicago, Boston, Philadelphia, Atlanta</h2> <p> The UCSC Bioinformatics Group announces six regional seminars and hands-on computer workshops on the UCSC Genome Browser, presented by <a href="http://www.openhelix.com/" target="_blank">OpenHelix:</a></p> @@ -19341,32 +19341,32 @@ The UCSC Genome Bioinformatics Group has released a Genome Browser for the <em>Drosophila simulans</em> draft genome sequence. The Release 1.0 assembly (UCSC version droSim1, Apr. 2005) was produced by the <a href="http://genome.wustl.edu/" target="_blank">Genome Sequencing Center</a> at the Washington University in St. Louis (WUSTL) School of Medicine. Release 1.0 represents a composite of several different <em>D. simulans</em> lines: contigs from the w501 line comprise the primary scaffolding, with contigs and unplaced reads from six other lines used to fill gaps in the w501 assembly.</p> <p> The total size of this assembly, excluding the gapless 14,972 bp mitochondrial sequence, is 142,405,747 bp including gaps and 127,241,461 bp excluding gaps. For more information about the <em>D. simulans</em> assembly and statistics, see the WUSTL Genome Sequencing Center <a href="http://genome.wustl.edu/genome.cgi?GENOME=Drosophila%20simulans%20White%20501" target="_blank"><em>Drosophila simulans</em></a> web page.</p> <p> Downloads of the droSim1 data and annotations may be obtained from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/droSim1/" target="_blank">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#droSim" target="_blank">Downloads</a> page. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/droSim1/" target="_blank">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#droSim" target="_blank">Downloads</a> page. The droSim1 annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> Thanks to the Genome Sequencing Center, WUSTL School of Medicine for providing this assembly. We'd also like to acknowledge the UCSC team who worked on this release: Angie Hinrichs, Jennifer Jackson, Ali Sultan-Qurraie, Brian Raney and Donna Karolchik. See the <a href="credits.html#droSim_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="053105"></a> <h2>May 31, 2005 June Genome Browser seminars in San Diego, CA and Salt Lake City, UT</h2> <p> The UCSC Bioinformatics Group announces two seminars and hands-on workshops on the UCSC Genome Browser, presented by <a href="http://www.openhelix.com/" target="_blank">OpenHelix</a>, a bioinformatics training, software testing and consulting company.</p> @@ -19399,86 +19399,86 @@ World monkey, which is a primate model organism, is important for the study of human biology and disease due to its genetic, physiologic and metabolic similarities to humans.</p> <p> Mmul_0.1 is a preliminary assembly using whole genome shotgun (WGS) reads from small and medium insert clones. Approximately 14.6 million reads were used in the assembly, representing about 12.6 Gb of sequence and about 4.6x coverage of the (clonable) genome. The total length of all contigs is approximately 2.7 Gb, or 2.8 Gb including gaps between contigs. Highly-repeated sequences and sequences from BAC clones were omitted from this assembly and will be placed in a subsequent version of the draft sequence.</p> <p> For more information about the rheMac1 assembly, see the Baylor <a href="http://www.hgsc.bcm.tmc.edu/projects/rmacaque/" target="_blank">Rhesus Monkey Project</a> web page.</p> <p> The rheMac1 sequence and annotation data can be downloaded from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/rheMac1/">FTP server</a> or the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#rhesus">Downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/rheMac1/">FTP server</a> or the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#rhesus">Downloads</a> page. These data have specific <a href="http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html" target="_blank">conditions for use</a>.</p> <p> Many thanks to Baylor College of Medicine, the Rhesus Monkey Genome Sequencing Consortium, and the other institutions who contributed to the sequencing and mapping effort of the Mmul_0.1 release. The UCSC Rhesus Genome Browser was produced by Robert Baertsch, Galt Barber, and Donna Karolchik. The initial set of rheMac1 annotation tracks was generated by the <a href="../staff.html">UCSC Genome Bioinformatics Group</a>. See the <a href="/goldenPath/credits.html#rhesus_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to the release of this browser.</p> <a name="050405"></a> <h2>May 5, 2005 New Mouse assembly available in Genome Browser</h2> <p> The latest mouse genome assembly from the Mouse Genome Sequencing Consortium, NCBI Build 34 (UCSC version mm6), is now available in the UCSC Genome Browser. In conjunction with this release, we have archived mouse assemblies mm3 and mm4. All archived assemblies are available for download via our -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#mouse" target="_blank">downloads +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#mouse" target="_blank">downloads server</a>.</p> <p> The Build 34 assembly has an assembled length of approximately 2.6 Gb, of which about 1.9 Gb is finished sequence. Chromosomes 2, 4, 11 and X are finished in this build. To review in-depth statistics on the assembly, see the NCBI <a href="https://www.ncbi.nlm.nih.gov/genome/guide/mouse/release_notes.html" target="_blank">Build 34 Data</a> web page. NOTE: In the Genome Browser mm6 assembly, chrY_random erroneously contains a region duplicated from chrY. For more information about this issue, see the Genome Browser <a href="../FAQ/FAQdownloads.html#download30">FAQ</a>. Please also note that the UCSC mm6 database contains only the reference strain C57BL/6J.</p> <p> The mm6 sequence and annotation data may be downloaded from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/mm6/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/mm6/">Downloads</a> web page. The mm6 annotation +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/mm6/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/goldenPath/mm6/">Downloads</a> web page. The mm6 annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> Mirror sites, please note: due to the size of the comparative genomics annotations in this assembly, the data set requires an unusually large amount of disk space. If you regularly download updates of the mouse data to your site, you may want to examine your available disk space before adding the annotation database from this assembly and/or reschedule your download for a period of low activity on your server. The size of the mm6 annotation database directory ($WEBROOT/goldenPath/mm6/database/) is approximately 93 GB. Including the related net and chains, the total size is 124 GB.</p> <p> We'd like to thank Deanna Church and the Mouse Genome Sequencing Consortium for this assembly. We'd also like to acknowledge the work of the UCSC mm6 team: Hiram Clawson, Fan Hsu, Jennifer Jackson, Robert Kuhn, Ali Sultan-Qurraie, Heather Trumbower and Donna Karolchik. For a complete list of the individuals and organizations who participated in this assembly, see the <a href="credits.html#mouse_credits">Credits</a> page.</p> <a name="050205"></a> <h2>May 2, 2005 Archiving mm3 and mm4 assemblies</h2> <p> To make room for the NCBI Build 34 mouse assembly (mm6, Mar. 2005), we are archiving the mm3 and mm4 mouse assemblies. These assemblies will remain available for download on our -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#mouse">downloads server</a>, although blat +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#mouse">downloads server</a>, although blat will no longer be supported. We plan to release the mm6 assembly in the next day or so.</p> <a name="032405"></a> <h2>Mar. 24, 2005 Genome Browser tutorial at Experimental Biology 2005 on Apr. 5</h2> <p> OpenHelix will be presenting a one-hour introductory seminar on the UCSC Genome Browser at the Experimental Biology 2005 meeting on 5 April, 5:00-6:00. The tutorial will cover the topics needed to effectively use the Browser, including basic functionality, searching and BLAT use, Table Browser use, creating and using Custom Tracks, and an introduction to the Gene Sorter.</p> <p> The free session will be conducted at the San Diego Convention Center, Room 12. For further information, visit the <a href="http://www.openhelix.com" target="_blank">OpenHelix website</a> or call 1-888-861-5051.</p> <p> OpenHelix will also be presenting brief introductory overviews of the UCSC Genome Browser in its @@ -19578,63 +19578,63 @@ <a name="022305"></a> <h2>Feb. 23, 2005 New Honeybee Genome Browser</h2> <p> The UCSC Genome Bioinformatics group has released a Genome Browser for a second honeybee assembly, Amel_2.0 (UCSC version apiMel2), produced by the Baylor College of Medicine Human Genome Sequencing Center.</p> <p> The assembly -- which is approximately 229 Mb in size including contig gaps -- was sequenced using a combined whole genome shotgun (WGS) and BAC clone approach. Overall sequence coverage is estimated at 7.5x. In this assembly, scaffolds have been arranged into 17 linkage groups that are somewhat equivalent to chromosomes. For more information about the assembly, see the Baylor <a href="http://www.hgsc.bcm.tmc.edu/projects/honeybee/" target="_blank">honeybee project</a> website.</p> <p> The apiMel2 sequence and annotation data can be downloaded from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/apiMel2/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#apiMel">downloads</a> page. Please see the +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/apiMel2/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#apiMel">downloads</a> page. Please see the Baylor <a href="http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html" target="_blank">conditions of use</a> page for guidelines regarding the use of these data.</p> <p> Many thanks to Baylor College of Medicine and the other institutions who contributed to the sequencing and mapping effort of the Amel_v2.0 release. The UCSC <em>A. mellifera</em> Genome Browser was produced by Andy Pohl, Angie Hinrichs, Jennifer Jackson, and Donna Karolchik. The initial set of apiMel2 annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the <a href="/goldenPath/credits.html#apiMel_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to the release of this browser.</p> <a name="021705"></a> <h2>Feb. 17, 2005 Cow Genome Browser released</h2> <p> The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server for the Sep. 2004 Btau_1.0 draft assembly of the cow genome. This assembly (UCSC version bosTau1) was provided by Baylor College of Medicine Human Genome Sequencing Center in Houston, TX.</p> <p> The Btau_1.0 release was assembled from whole genome shotgun (WGS) reads using the Atlas genome assembly system. Several WGS libraries, with inserts of 2 - 4 kb and 4 - 6 kb, were used to produce the data. Approximately 15 million reads were assembled, representing about 9 Gb of sequence and 3x coverage of the (clonable) bovine genome. Highly repeated sequences and BAC clones sequences were omitted from this assembly; these will be placed in a subsequent version of the draft sequence. The assembly contains approximately 450,000 scaffolds.</p> <p> For more information on the Btau_1.0 assembly, see the Baylor <a href="http://www.hgsc.bcm.tmc.edu/projects/bovine/" target="_blank">Bovine Genome Project</a> web page.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/bosTau1/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#cow">Downloads</a> page. Please refer to the +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/bosTau1/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#cow">Downloads</a> page. Please refer to the Baylor <a href="http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html" target"_blank">conditions of use</a> regarding these data. The bosTau1 annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> We'd like to thank Baylor College of Medicine for the bovine sequence and assembly. We'd also like to acknowledge the members of the UCSC Genome Bioinformatics Group who contributed to the Cow Genome Browser: Heather Trumbower, Jim Kent, Hiram Clawson, Angie Hinrichs, Brian Raney, Mark Diekhans, Robert Kuhn, Ali Sultan-Qurraie, and Donna Karolchik. See the <a href="/goldenPath/credits.html#cow_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="021505"></a> <h2>Feb. 15, 2005 UniProt (Swiss-Prot/TrEMBL) display changes</h2> <p> We have made several adjustments to the Genome Browser databases to accommodate recent changes to @@ -19660,56 +19660,56 @@ <p> The Release 4 euchromatic sequence, 118.4 Mb in size, contains six euchromatic chromosome arms with a total of 23 sequence gaps. The assembly was validated in collaboration with the Genome Sciences Centre at the British Columbia Cancer Agency in Vancouver, Canada, using fingerprint analysis of a tiling path of BACs spanning the genome.</p> <p> The Release 3.2 heterochromatic sequence is based on 20.7 Mb of Release 3 whole genome shotgun scaffolds from Celera that could not be assembled into the euchromatin arms, as well as a few BDGP-sequenced scaffolds. The scaffolds have been assigned to chromosomes where possible.</p> <p> For more information on this assembly, see the release notes for the <a href="http://www.fruitfly.org/annot/release4.html" target="_blank">Release 4 euchromatic sequence</a>.</p> <p> Downloads of the dm2 data and annotations may be obtained from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/dm2/" target="_blank">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#fruitfly">Downloads</a> page. The dm2 +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/dm2/" target="_blank">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#fruitfly">Downloads</a> page. The dm2 annotation tracks were provided by FlyBase or generated by UCSC.</p> <p> Thanks to BDGP, DHGP, and the Flybase Consortium for providing the sequence, assembly, gene annotations and analysis of this genome. The UCSC Genome Browser team is Angie Hinrichs, Brian Raney, Galt Barber, and Donna Karolchik. See the <a href="/goldenPath/credits.html#dm_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="011805"></a> <h2>Jan. 18, 2005 Opossum Genome Browser</h2> <p> The opossum (<em>Monodelphis domestica</em>) is the latest vertebrate addition to the UCSC Genome Browser genome collection. The Oct. 2004 preliminary assembly -- UCSC version monDom1 -- was sequenced and assembled by <a href="http://www.broad.mit.edu/seq/" target="_blank">The Broad Institute</a>, Cambridge, MA, USA.</p> <p> This preliminary draft was assembled from 33,507,069 placed reads, and consists of 109,065 contigs containing a total of 3,492,108,230 bases. There are 3,563,247,205 total bases in the 19,348 scaffolds in the assembly, with 71,138,975 bases in the gaps between contigs within the scaffolds. The scaffolds range in size from 1,000 bases to 22,286,839 bases.</p> <p> The monDom1 sequence and annotation data can be downloaded from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/monDom1/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#opossum">downloads</a> page. Please review +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/monDom1/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#opossum">downloads</a> page. Please review the <a href="/goldenPath/credits.html#opossum_use" target="_blank">guidelines</a> for using these data.</p> <p> Many thanks to The Broad Institute for providing these data. The UCSC opossum Genome Browser was produced by Hiram Clawson, Galt Barber, Ali Sultan-Qurraie, Brian Raney and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the <a href="/goldenPath/credits.html#opossum_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to the release of this browser.</p> <!---------------- 2004 archived news ---------------> <a name="2004"></a> <a name="122304"></a> <h2>Dec. 23, 2004 Updated Zebrafish assembly (Zv4) now available</h2> <p> @@ -19727,32 +19727,32 @@ this assembly were identical to those used for the Zv3 assembly, but the FPC data and its integration with the WGS data has been considerably improved.</p> <p> The Sanger Institute notes that there is high level of misassembly present in this release due to the large amount of polymorphism in the DNA source. Highly variable regions within the genome posed assembly difficulties, most likely because the sequences originated from different haplotypes. For more information about this assembly, see the Sanger Institute web page for the <a href="http://www.sanger.ac.uk/Projects/D_rerio/" target="_blank"><em>Danio rerio</em> Sequencing Project</a>.</p> <p> In addition to the assembly improvements noted above, a new zebrafish repeat library was used to mask repeats in the danRer2 Genome Browser, resulting in a cleaner set of alignments containing considerably less "noise".</p> <p> The danRer2 sequence and annotation data can be downloaded from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/danRer2/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#zebrafish">downloads</a> page. Please review +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/danRer2/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#zebrafish">downloads</a> page. Please review the <a href="http://www.sanger.ac.uk/Projects/use-policy.shtml" target="_blank">guidelines</a> for using these data.</p> <p> We'd like to thank the Wellcome Trust Sanger Institute, the Max Planck Institute for Developmental Biology, Hubrecht Laboratory and the other institutions who contributed to the sequencing and mapping effort of this release. Special thanks to the Zebrafish Genome Initiative at Children's Hospital in Boston for their collaboration on this release. The UCSC zebrafish Genome Browser was produced by Rachel Harte, Mark Diekhans, Heather Trumbower, Jennifer Jackson, and Donna Karolchik. The initial set of annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the <a href="/goldenPath/credits.html#zebrafish_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to the release of this browser.</p> <a name="122204"></a> <h2>Dec. 22, 2004 UCSC releases Honeybee Browser</h2> <p> @@ -19760,32 +19760,32 @@ assembly produced by the Baylor College of Medicine Human Genome Sequencing Center.</p> <p> The assembly -- which is approximately 213 Mb in size including contig gaps -- was sequenced using a combined whole genome shotgun (WGS) and BAC clone approach. The BAC clone sequence was produced following a pooled-array strategy. Overall sequence coverage is estimated at 6X. For more information about this assembly, see the Baylor <a href="http://www.hgsc.bcm.tmc.edu/projects/honeybee/" target="_blank">honeybee project</a> website.</p> <p> The honeybee genome is of interest to the agricultural community, in addition to its role as a model organism in the study of several human health issues, including immunity, allergic reaction, antibiotic resistance, development, mental health, longevity, and diseases of the X chromosome. The honeybee is also interesting for its social and behavioral traits.</p> <p> The apiMel1 sequence and annotation data can be downloaded from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/apiMel1/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#apiMel">downloads</a> page. Please see the +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/apiMel1/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#apiMel">downloads</a> page. Please see the Baylor <a href="http://www.hgsc.bcm.tmc.edu/projects/conditions_for_use.html" target="_blank">conditions of use</a> page for guidelines regarding the use of these data.</p> <p> Many thanks to Baylor, Children's Hospital Oakland Research Institute (CHORI), and the other institutions who contributed to the sequencing and mapping effort of the Amel_1.2 release. The UCSC <em>A. mellifera</em> Genome Browser was produced by Angie Hinrichs, Brian Raney, Robert Kuhn, and Donna Karolchik. The initial set of apiMel1 annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the <a href="/goldenPath/credits.html#apiMel_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to the release of this browser.</p> <a name="121504"></a> <h2>Dec. 15,2004 Three new Drosophila assemblies in Genome Browser</h2> <p> The UCSC Genome Bioinformatics Group has added three more Drosophila genomes to the UCSC Genome @@ -19801,32 +19801,32 @@ details about an individual genome, refer to the Genome Browser <a href="../cgi-bin/hgGateway?org=D.+ananassae">gateway</a> page associated with the assembly.</p> <p> In upcoming months, UCSC plans to provide several additions and enhancements to the Drosophila browsers: </p> <ul> <li> additional Drosophila genomes, including <em>D. erecta</em> and <em>D. simulans</em></li> updated versions of <em>D. melanogaster</em> and other genomes</li> <li> multiple alignments of all fly assemblies from the 12-Drosophila project to <em>D. melanogaster</em> </ul> <p> Sequence and annotation data for all the Drosophila assemblies can be downloaded from the UCSC -Genome Browser <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html">downloads</a> page. Please review the data +Genome Browser <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html">downloads</a> page. Please review the data use guidelines outlined in the README.txt files that accompany the downloads. The data use restrictions are also available on the Genome Browser <a href="/goldenPath/credits.html">credits</a> page.</p> <p> We'd like to thank Agencourt Bioscience Corporation, TIGR, and other institutions who contributed to the sequencing and mapping effort for these assemblies. The UCSC Drosophila browsers were produced by Angie Hinrichs, Brian Raney, Heather Trumbower, Robert Kuhn, Galt Barber, Jennifer Jackson, Ali Sultan-Qurraie, and Donna Karolchik. The UCSC Genome Bioinformatics Group generated the initial set of annotation tracks. See the <a href="/goldenPath/credits.html">credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="120304"></a> <h2>Dec. 3, 2004 SNP track for Build 35 (hg17) assembly released</h2> <p> UCSC has released the much-awaited SNP annotation track for the Build 35 (hg17) Human Genome @@ -19842,32 +19842,32 @@ <a name="111704"></a> <h2>Nov. 17, 2004 <em>X. tropicalis</em> v.3.0 released in Genome Browser</h2> <p> The v.3.0 <em>Xenopus tropicalis</em> assembly is now available on the UCSC Genome Browser. This whole genome shotgun assembly (xenTro1, Oct. 2004) was provided by the U.S. DOE Joint Genome Institute (JGI).</p> <p> Version 3.0 was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 7.4X. After trimming for vector and quality, 19.1 million reads assembled into 27,064 scaffolds totaling 1.63 Gbp. Roughly half the genome is contained in 392 scaffolds, each of which is at least 1.2 Mb in length. For more information about this assembly, see the JGI <a href="http://genome.jgi-psf.org/Xentr3/Xentr3.home.html" target="_blank"><em>X. tropicalis</em> website</a>.</p> <p> The xenTro1 sequence and annotation data can be downloaded from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/xenTro1/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#xenTro">downloads</a> page. Please see the +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/xenTro1/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#xenTro">downloads</a> page. Please see the JGI <a href="http://genome.jgi-psf.org/Xentr3/Xentr3.download.html" target="_blank">data release policy</a> for data use guidelines.</p> <p> Many thanks to JGI and the other institutions who contributed to the sequencing and mapping effort of the v. 3.0 release. The UCSC <em>X. tropicalis</em> Genome Browser was produced by Fan Hsu, Jim Kent, Heather Trumbower, Hiram Clawson, Brian Raney, Galt Barber, Mark Diekhans, Angie Hinrichs, and Donna Karolchik. The initial set of xenTro1 annotation tracks was generated by the UCSC Genome Bioinformatics Group. See the <a href="/goldenPath/credits.html#xenTro_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to the release of this browser.</p> <h2>Nov. 17,2004 Genome Browser tutorial offered at ASCB meeting</h2> <p> OpenHelix will be presenting the tutorial "Introduction to the UCSC Genome Browser" at the American Society for Cell Biology (ASCB) Annual Meeting in Washington, D.C. on Dec. 5, 8:30 - 10:00 @@ -19975,32 +19975,32 @@ <h2>Sep. 10, 2004 <em>T. nigroviridis</em> genome now available in Genome Browser</h2> <p> The Genoscope v7 <em>Tetraodon nigroviridis</em> genome assembly is now available in the UCSC Genome Browser and Blat server. This assembly, UCSC version tetNig1 dated Feb. 2004, is the result of a collaboration between <a href="http://www.genoscope.cns.fr/" target="_blank">Genoscope</a> and the <a href="http://www.broad.mit.edu/annotation/tetraodon/background.html" target="_blank">Broad Institute</a> of MIT and Harvard.</p> <p> The v7 assembly was constructed using the whole genome shotgun (WGS) approach, resulting in a sequence coverage of about 7.9X. The assembly contains 45,609 contigs and 25,773 scaffolds generated by the Arachne program and covers more than 90% of the genome. Additional linking data were used to build ultracontigs and to organize the assembly into chromosomes. Genoscope estimates the size of the Tetraodon genome to be about 385 Mb.</p> <p> Downloads of the tetNig1 data and annotations may be obtained from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/tetNig1/" target="_blank">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#tetraodon" target="_blank">Downloads</a> +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/tetNig1/" target="_blank">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#tetraodon" target="_blank">Downloads</a> page. These data have been freely provided by Genoscope before publication with <a href="/goldenPath/credits.html#tetraodon_credits" target="_blank">specific conditions for use</a>. The initial set of annotation tracks were generated by Genoscope and the UCSC Bioinformatics Group based on data provided Genoscope. Tetraodon gene predictions generated by Genoscope using <a href="http://www.sanger.ac.uk/Software/analysis/GAZE/" target="_blank">GAZE</a> will be available in the Genome Browser within a few weeks.</p> <p> Many thanks to Genoscope and the Broad Institute of MIT and Harvard for this genome assembly. The UCSC team who produced this browser are Rachel Harte, Robert Kuhn, Donna Karolchik, and the Genome Browser sysadmin team. See the <a href="/goldenPath/credits.html#tetraodon_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="090104"></a> <h2>Sep. 1,2004 Genome Browser released for <em>D. pseudoobscura</em> draft assembly</h2> @@ -20011,32 +20011,32 @@ <p> Freeze 1 is a whole genome shotgun assembly produced using Baylor HGSC's assembly engine, Atlas. The assembly, which provides approximately 7x coverage of the euchromatic portion of the genome, contains 759 scaffolds. The scaffold N50 size is 1,018,646 bp. The total scaffold size for this assembly is 139.3 Mbp, with an average size of 184,465 bp. Due to an assembly error, four large scaffolds "jumped" chromosomes. These have been split into "A" and "B" parts in the downloadable assembly files. See the gateway page for more information.</p> <p> Baylor HGSC has provided a <a href="ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Dpseudoobscura/fasta/D_pseudo_freeze1_scaffold_to_chromosome_assignments_8_28_03.txt" target="_blank">putative chromosome assignment</a> for the majority of larger scaffolds (> 90% of unique sequence), based on conservation between the Muller elements.</p> <p> Downloads of the dp2 data and annotations may be obtained from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/dp2/" target="_blank">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#dp">Downloads</a> page. The initial set of +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/dp2/" target="_blank">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#dp">Downloads</a> page. The initial set of annotation tracks were generated by UCSC.</p> <p> Many thanks to the Baylor HGSC for providing the genome assembly data. The UCSC team who produced this browser are Angie Hinrichs, Heather Trumbower, Robert Kuhn, Donna Karolchik, and the Genome Browser sysadmin team. See the <a href="/goldenPath/credits.html#dp_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="083004"></a> <h2>Aug. 30, 2004 Genome Browser seminars - Seattle and San Francisco</h2> <p> The UCSC Bioinformatics Group announces 2 seminars and hands-on workshops on the UCSC Genome Browser, presented by <a href="http://www.openhelix.com/" target="_blank">OpenHelix</a>, a bioinformatics training, software testing and consulting company.</p> <p> These introductory sessions are geared towards anyone with a basic knowledge of genomic and @@ -20066,109 +20066,109 @@ Ensembl.</p> <p> The MOZ2 assembly is a 10x whole genome shotgun assembly. The assembled portion of the genome is about 278 Mbp in length with a total of 8,987 unique scaffolds, the largest scaffold being 23.1 Mbp. Approximately 85% of the sequence has been assigned to chromosomal locations. Chromosome arms chr2L, chr2R, chr3L, chr3R, and chrX are represented by 13, 49, 42, 28, and 10 large scaffolds respectively. No scaffolds have yet been assigned to the Y chromosome. The unassigned scaffolds, concatenated together in arbitrary order, can be found in the artificial unknown "chromosome" chrUn.</p> <p> For more information about the initial <em>A. gambaie</em> assembly, see Holt et al. (2002), <a href="http://www.sciencemag.org/cgi/content/abstract/298/5591/129" target="_blank">The Genome Sequence of the Malaria Mosquito Anopheles gambiae</a>, <em>Science</em> 2002 298:129-149.</p> <p> Downloads of the anoGam1 data and annotations may be obtained from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/anoGam1/" target="_blank">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#anoGam">Downloads</a> page. The anoGam1 +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/anoGam1/" target="_blank">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#anoGam">Downloads</a> page. The anoGam1 annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> Many thanks to the International Anopheles Genome Project and Ensembl for providing the sequence of this genome. The UCSC team who produced this browser are Angie Hinrichs, Galt Barber, Donna Karolchik, and sysadmins Paul Tatarsky and Jorge Garcia. See the <a href="/goldenPath/credits.html#anoGam_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to this release.</p> <a name="072904"></a> <h2>Jul. 29, 2004 Zebrafish Genome assembly Zv3 now available in Genome Browser</h2> <p> The Zv3 Zebrafish genome assembly (UCSC version danRer1) is now available on the UCSC Genome Browser and Blat server. This assembly was produced by The Wellcome Trust Sanger Institute, Hinxton, UK, in collaboration with the Max Planck Institute for Developmental Biology in Tuebingen, Germany, and the Netherlands Institute for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands.</p> <p> The Zv3 assembly consists of 1,459,115,486 bp in 58,339 supercontigs, with a sequence coverage of approximately 5.7X. This zebrafish assembly is the first to be tied to the FPC map: 1,083,447,588 bp (74%) of the sequence were mapped in this way. Please note that this is a preliminary assembly; a high level of misassembly is present due to polymorphisms in the DNA source.</p> <p> For more information about this assembly, see the Sanger Institute's <a href="http://www.sanger.ac.uk/Projects/D_rerio/" target="_blank"><em>Danio rerio</em> Sequencing Project</a> web page. UCSC plans to release the Zv4 version of the zebrafish assembly on the Genome Browser in Fall '04.</p> <p> Downloads of the Zebrafish data and annotations can be obtained from the UCSC -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/danRer1/" target="_blank">FTP site</a> or -<a href=http://hgdownload.soe.ucsc.edu/downloads.html#zebrafish>Downloads page</a>. The danRer1 +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/danRer1/" target="_blank">FTP site</a> or +<a href=http://hgdownload.gi.ucsc.edu/downloads.html#zebrafish>Downloads page</a>. The danRer1 annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="/goldenPath/credits.html#zebrafish_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to the success of this release.</p> <p> We'd like to thank The Wellcome Trust Sanger Institute and their collaborators for providing this assembly. A special thanks to Yi Zhou, Anthony DiBiase and Leonard Zon from the Children's Hospital in Boston, MA, USA for their collaboration on this release. The UCSC Zebrafish Genome Browser team is Rachel Harte, Heather Trumbower, and Donna Karolchik.</p> <a name="072304b"></a> <h2>Jul. 23, 2004 Latest Human Genome reference sequence now in Browser</h2> <p> The latest human genome reference sequence (NCBI Build 35, May 2004) is now available as database hg17 in the UCSC Genome Browser and Blat server. This sequence was obtained from NCBI and was produced by the International Human Genome Sequencing Consortium.</p> <p> Bulk downloads of the data are available via FTP at -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg17">ftp://hgdownload.soe.ucsc.edu/goldenPath/hg17</a> +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg17">ftp://hgdownload.gi.ucsc.edu/goldenPath/hg17</a> or through the Downloads link on this page. We recommend that you use FTP rather than HTML for the download of large or multiple files.</p> <p> We'd like to thank NCBI and the International Human Genome Sequencing Consortium for furnishing the data, and the UCSC team members who contributed to this release: Hiram Clawson, Terry Furey, Heather Trumbower, Robert Kuhn, Donna Karolchik, Kate Rosenbloom, Angie Hinrichs, Rachel Harte, Jim Kent and our sysadmin team Patrick Gavin, Jorge Garcia, and Paul Tatarsky.</p> <a name="072304a"></a> <h2>Jul. 23, 2004 <em>D. yakuba</em> added to Genome Browser</h2> <p> The UCSC Genome Bioinformatics Group has released a Genome Browser and Blat server on a second species of fruitfly, <em>D. yakuba</em>. The April 2004 Release 1.0 of this genome (UCSC version droYak1) was sequenced and assembled by the Genome Sequencing Center, Washington University (WUSTL) School of Medicine in St. Louis.</p> <p> <em>D. yakuba</em> is closely related to the model organism, <em>D. melanogaster</em>, with which it shared a common ancestor approximately 10 million years ago. The <em>D. yakuba</em> genome is largely alignable to the <em>D. melanogaster</em> genome, but differs sufficiently to offer an interesting study of sequence divergence between the two species. <em>D. yakuba</em> occupies a critical intermediate position among several Drosophila species that will facilitate evolutionary studies among the fruitflies. For information about the <em>D. yakuba</em> assembly and statistics, see the WUSTL Genome Sequencing Center <a href="http://genome.wustl.edu/genome.cgi?GENOME=Drosophila%20yakuba&GROUP=6" target="_blank"><em>Drosophila yakuba</em></a> web page.</p> <p> Downloads of the droYak1 data and annotations can be obtained from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/droYak1/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#droYak">Downloads</a> page. The droYak1 +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/droYak1/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#droYak">Downloads</a> page. The droYak1 annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> Thanks to the Genome Sequencing Center at WUSTL School of Medicine for providing the sequence and assembly of this genome. The UCSC <em>D. yakuba</em> Genome Browser was produced by Angie Hinrichs, Michael Chalup, and Donna Karolchik. See the <a href="/goldenPath/credits.html#droYak_credits">Credits</a> page for a detailed list of the organizations and individuals who contributed to the success of this release.</p> <a name="071604"></a> <h2>Jul. 16, 2004 Genome Browser released for mouse assembly NCBI Build 33</h2> <p> The latest mouse assembly -- Build 33 from NCBI (UCSC version mm5) -- is now available via the UCSC Genome Browser and Blat server. This assembly includes approximately 2.6 gigabases of sequence. Chromosome 11 is finished in Build 33; the Sanger Institute has provided a corresponding agp file. The whole genome N50 for this assembly is 22.3 Mb, in comparison to 17.7 Mb for the previous build. @@ -20177,92 +20177,92 @@ This assembly is a composite version in which phase 3 High Throughput Genome Sequence (HTGS) was merged with the Mouse Genome Sequencing Consortium v3 Whole Genome Shotgun Assembly (MGSCv3). The assembly was performed by NCBI using a "combined" tiling path that was created automatically for the most part, but was manually curated in places. This facilitated the placement of finished sequence in the context of the MGSCv3 assembly. Draft sequence was not included in this build: the slight increase in coverage gained by using this would have been offset by the increase in build errors.</p> <p> More information about Build 33 will be available soon in the NCBI <a href="https://www.ncbi.nlm.nih.gov/genome/seq/NCBIContigInfo.html" target="_blank">assembly notes</a> and <a href="https://www.ncbi.nlm.nih.gov/mapview/stats/BuildStats.cgi?taxid=10090&build=33&ver=1" target="_blank">Build 33 statistics</a>.</p> <p> The mm5 sequence and annotation data may be downloaded from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/mm5/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/mm5/">Downloads</a> web page. The mm5 annotation +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/mm5/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/goldenPath/mm5/">Downloads</a> web page. The mm5 annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> We'd like to thank Deanna Church, Richa Agrawala, and the Mouse Genome Sequencing Consortium for this assembly. We'd also like to acknowledge the work of the UCSC mm5 team: Fan Hsu, Hiram Clawson, Angie Hinrichs, Heather Trumbower, Mark Diekhans, Donna Karolchik and our systems administrators Jorge Garcia, Patrick Gavin and Paul Tatarsky.</p> <a name="071504"></a> <h2>Jul. 15, 2004 <em>C. intestinalis</em> v1.0 released in Genome Browser</h2> <p> The v1.0 <em>C. intestinalis</em> draft assembly from the US DOE Joint Genome Institute is now available for study using the UCSC Genome Browser and Blat server (UCSC database ci1).</p> <p> The whole genome shotgun assembly was constructed with the JGI assembler (JAZZ) paired-end sequencing reads at a coverage of 8.2X. The draft contains 116.7 million bp of nonrepetitive sequence in 2,501 scaffolds greater than 3 kb. 60 Mbp of this has been assembled into 117 scaffolds longer than 190 Kbp, and 85% of the assembly (104.1 Mbp) is found in 905 scaffolds longer than 20 kb. The assembly, gene modeling and analysis were performed at the JGI.</p> <p> For more information about the ci1 assembly, see the JGI <a href="http://genome.jgi-psf.org/ciona4/ciona4.info.html" target="_blank"><em>C. intestinalis</em> project page</a>. Additional information and an analysis of the euchromatic regions of this genome may be found in Dehal et al., <a href="http://www.sciencemag.org/cgi/content/full/298/5601/2157" target="_blank">The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins</a>. Science. 2002 Dec 13;298(5601):2157-67.</p> <p> Bulk downloads of the sequence and annotation data are available via the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/ci1/" target="_blank">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#ciona" target="_blank">Downloads page</a>. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/ci1/" target="_blank">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#ciona" target="_blank">Downloads page</a>. The ci1 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.</p> <p> Many thanks to the JGI and their collaborators for providing the v1.0 sequence and annotations. The ci1 Genome Browser was produced by Brian Raney, Galt Barber, Heather Trumbower, Robert Kuhn, Donna Karolchik and the Genome Browser sysadmin team - Patrick Gavin, Jorge Garcia, and Paul Tatarsky. We'd also like to thank Tom Pringle for his technical input and Mark Diekhans for his work on the incremental updates for this release.</p> <a name="071404"></a> <h2>Jul. 14, 2004 Genome Browser released for dog draft assembly v1.0</h2> <p> UCSC has released a Genome Browser and Blat server on the July 2004 v1.0 dog genome sequenced and assembled by the Broad Institute of MIT and Harvard and Agencourt Bioscience. The whole genome shotgun (WGS) sequence is based on 7.6X coverage of the dog genome, assuming a WGS assembly size of 2.4 Gb. The assembly has an N50 contig length of 123 kb and an N50 supercontig length of 41.6 Mb.</p> <p> The dog genome, which contains approximately 2.5 billion base pairs, is similar in size to the genomes of humans and other mammals. The boxer breed was selected for the initial sequencing effort, based on the lower variation rate in its genome relative to other breeds. In addition to the boxer, samples from nine other dog breeds, four wolves and a coyote are being used to generate an initial set of single nucleotide polymorphisms (SNPs) to facilitate disease studies. The SNPs should be available soon from <a href="https://www.ncbi.nlm.nih.gov/SNP/" target="_blank">dbSNP</a>.</p> <p> For more information about the dog draft assembly, see the <a href="http://www.genome.gov/12511476" target="_blank">NHGRI press release</a>.</p> <p> The dog sequence and annotation data can be downloaded from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/canFam1/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#dog">downloads</a> page. These data have +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/canFam1/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#dog">downloads</a> page. These data have <a href="/goldenPath/credits.html#dog_use">specific conditions for use</a>.</p> <p> Many thanks to the Broad Institute of MIT and Harvard, NHGRI, Agencourt Bioscience, Children's Hospital Oakland Research Institute, Centre National de la Recherche Scientifique, North Carolina State University, and Fred Hutchinson Cancer Research Center for their contributions to the sequencing, assembly, and mapping efforts. The initial canFam1 annotation track set, generated by the UCSC Genome Bioinformatics Group, will soon be supplemented by annotations from collaborators worldwide. See the <a href="/goldenPath/credits.html#dog_credits">credits</a> page for a detailed list of the organizations and individuals who contributed to the success of this release.</p> <a name="062404"></a> <h2>Jun. 24, 2004 ENCODE project featured in Genome Browser</h2> <p> We'd like to announce the release of UCSC Genome Browser features tailored to the ENCODE project community, including an <a href="/ENCODE/">ENCODE-specific page</a> to highlight the ENCODE @@ -20306,55 +20306,55 @@ What's in a name? In an effort to clarify the role of the UCSC Family Browser, we have changed its name to the UCSC Gene Sorter. We think this name better describes this tool, which lets the user collect information on groups of genes that may be related in many different ways. The Gene Sorter provides a wealth of information on gene expression, protein homology (both within and across species), GO terms, and Pfam domains, cross links to many other databases, and much more.</p> <p> If you haven't already tried this tool, we encourage you to give it a spin. You'll find it at <a href="../cgi-bin/hgNear">http://genome.ucsc.edu/cgi-bin/hgNear</a>, or click the "Gene Sorter" link on any Genome Browser menu bar.</p> <a name="052704"></a> <h2>May 27, 2004 New Genome Browser downloads server</h2> <p> As a follow-up to last week's FTP site switch, we are changing the location of the UCSC Genome Browser downloads site to -<a href="http://hgdownload.soe.ucsc.edu/">http://hgdownload.soe.ucsc.edu/</a>. All downloadable +<a href="http://hgdownload.gi.ucsc.edu/">http://hgdownload.gi.ucsc.edu/</a>. All downloadable files currently located in http://genome.ucsc.edu/goldenPath will be moved to the new server. Please make a note of the new URL and update any references to it. Users accessing downloads through -the Genome Browser <a href="http://hgdownload.soe.ucsc.edu/downloads.html">Downloads page</a> will +the Genome Browser <a href="http://hgdownload.gi.ucsc.edu/downloads.html">Downloads page</a> will be redirected automatically to the new location.</p> <a name="051904"></a> <h2>May 19, 2004 New Genome Browser FTP server</h2> <p> We have changed the URL for the UCSC Genome Browser ftp site to -<a href="ftp://hgdownload.soe.ucsc.edu/">ftp://hgdownload.soe.ucsc.edu/</a>. This replaces the old +<a href="ftp://hgdownload.gi.ucsc.edu/">ftp://hgdownload.gi.ucsc.edu/</a>. This replaces the old URL of ftp://genome.ucsc.edu/. The old URL will be disabled within a few days. Please make a note of the new URL and update any references to it.</p> <a name="051104"></a> <h2>May 11, 2004 <em>C. elegans</em> WS120 added to Genome Browser</h2> <p> UCSC has released a Genome Browser and Blat server on an updated version of the <em>C. elegans</em> genome. The March 2004 assembly -- UCSC version ce2 -- is based on sequence version WS120 deposited into <a href="http://www.wormbase.org/species/c_elegans" target="_blank">WormBase</a> as of Mar. 1, 2004. This assembly has a finishing error rate of 1:10,000.</p> <p> The ce2 sequence and annotation data may be downloaded from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/ce2/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#c_elegans">Downloads</a> web page. The ce2 +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/ce2/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#c_elegans">Downloads</a> web page. The ce2 annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> We'd like to thank the <a href="http://genome.wustl.edu/" target="_blank">Genome Sequencing Center</a> at Washington University in St. Louis and the <a href="http://www.sanger.ac.uk/" target="_blank">Sanger Institute</a> for their collaborative work in sequencing the <em>C. elegans</em> genome. Many thanks to the <a href="http://www.wormbase.org/wiki/index.php/WormBase_Consortium" target="_blank">WormBase consortium</a> for making the worm sequence publicly available. We'd also like to acknowledge the UCSC team who contributed to this release: Rachel Harte (lead engineer), Hiram Clawson (WABA and miRNA annotations), Mike Chalup (QA), Galt Barber (QA), Heather Trumbower (QA), and Donna Karolchik (documentation).</p> <a name="042204"></a> <h2>Apr. 22, 2004 Mouse Genome assembly added to Proteome Browser</h2> <p> @@ -20466,32 +20466,32 @@ intermediate data point between mouse and fugu. Comparative genomics analyses between the chicken and other sequenced organisms should yield valuable information on the evolution of gene order and arrangement, thus improving our understanding of the structure and function of genes. /<p> <p> To facilitate comparative genomics studies, alignments of the chicken sequence to the human genome will be available in the Genome Browser later this week. Downloads of the comparative data are currently available through the Downloads page (see below).</p> <p> For more information about the release of the chicken genome assembly, see the NHGRI <a href="http://www.nhgri.nih.gov/11510730" target="_blank">press release</a>. Additional background on the rationale behind the chicken genome sequencing effort can be found in the <a href="http://www.genome.wustl.edu/ancillary/data/whitepapers/Gallus_gallus_WP.pdf" target="_blank">sequencing proposal</a>.</p> <p> Bulk downloads of the chicken sequence and annotations may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/galGal2/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#chicken">Downloads</a> page. These data +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/galGal2/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#chicken">Downloads</a> page. These data have <a href="/goldenPath/credits.html#chicken_use">specific conditions for use</a>.</p> <p> We'd like to thank the Genome Sequencing Center at the Washington University School of Medicine in St. Louis, Wageningen University, and the Chicken Mapping Consortium for providing these data. The chicken browser annotation tracks were generated by UCSC and collaborators worldwide. See the <a href="/goldenPath/credits.html#chicken_credits">Credits</a> page for a detailed list of acknowledgements. The UCSC Chicken Genome Browser was produced by Angie Hinrichs, Heather Trumbower, Rachel Harte, and Donna Karolchik.</p> <a name="022304"></a> <h2>Feb. 23, 2004 Chimpanzee genome browser released</h2> <p> We are happy to announce the release of a Genome Browser and Blat server for the chimpanzee (<em>Pan troglodytes</em>). The 13 Nov. 2003 Arachne assembly -- labeled Chimp Build 1 Version 1 (UCSC version panTro1) -- was produced by the Chimpanzee Genome Sequencing Consortium.</p> @@ -20503,32 +20503,32 @@ (<em>Pan troglodytes verus</em>). <a href="http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/ChimpGenome2.pdf" target="_blank">Background information</a> on the chimp genome sequencing project and the <a href="http://www.genome.gov/11509418" target="_blank">initial news release</a> about the chimp assembly can be found on the NHGRI website.</p> <p> Research has indicated that the human and chimp genomes probably differ by approximately one percent. Because of this close relationship between chimpanzees and humans, the assembly should facilitate comparative analyses of the two genomes that have not been possible with other species that have been sequenced to date.</p> <p> The initial release of the Chimp Browser provides several annotation tracks comparing the chimp and human genomes. More comparative annotations will be added in upcoming weeks.</p> <p> Bulk downloads of the chimp sequence and annotations may be obtained from the Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/panTro1/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#chimp">Downloads</a> page. The complete set +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/panTro1/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#chimp">Downloads</a> page. The complete set of sequence reads is available at the <a href="https://www.ncbi.nlm.nih.gov/Traces" target="_blank">NCBI trace archive</a>. Blat searches on chrUn_random are not supported in the initial release, but will be available soon.</p> <p> We'd like to thank NHGRI, the Broad Institute at MIT/Harvard, and Washington University at St. Louis School of Medicine for providing this sequence, and LaDeana Hillier, Washington University School of Medicine, and the Broad Institute for their work on the alignments. The chimpanzee browser annotation tracks were generated by UCSC and collaborators worldwide.</p> <p> The UCSC team who worked on this release consisted of Kate Rosenbloom, Jim Kent, Hiram Clawson, Heather Trumbower, Robert Kuhn, Donna Karolchik, and the Genome Browser sysadmin team.</p> <a name="021204"></a> <h2>Feb. 12, 2004 New UCSC supported mirror site</h2> <p> @@ -20581,122 +20581,122 @@ This assembly (UCSC version sacCer1) is based on sequence dated 1 Oct. 2003 in the <a href="http://www.yeastgenome.org/" target="_blank">Saccharomyces Genome Database</a> (SGD). The sequence, open reading frame (ORF), and gene annotations were downloaded from the site <a href="ftp://genome-ftp.stanford.edu/pub/yeast/data_download" target="_blank">ftp://genome-ftp.stanford.edu/pub/yeast/data_download</a>.</p> <p> The S288C strain was used in this sequencing project. Reference information for each chromosome may be found in the SGD <a href="http://www.yeastgenome.org/chromosomes.shtml" target="_blank">Systematic Sequencing Table</a>. For more information about the yeast genetic and physical maps, see the paper Cherry JM et al. <a href="http://db.yeastgenome.org/cgi-bin/SGD/reference/reference.pl?refNo=22828" target="_blank">Genetic and physical maps of Saccharomyces cerevisiae</a>. <em>Nature</em> 1997 387(6632 Suppl):67-73.</p> <p> Downloads of the yeast data and annotations may be obtained from the UCSC Genome Browser -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/sacCer1/">FTP server</a> or -<a href="http://hgdownload.soe.ucsc.edu/downloads#yeast">Downloads</a> page.</p> +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/sacCer1/">FTP server</a> or +<a href="http://hgdownload.gi.ucsc.edu/downloads#yeast">Downloads</a> page.</p> <p> We'd like to thank Stanford University, the SGD, the University of California San Francisco (UCSF), Washington University in St. Louis, and the Broad Institute at MIT/Harvard for providing the data and annotations for this assembly. We'd also like to acknowledge the UCSC team who worked on this release: Jim Kent, Heather Trumbower, Robert Kuhn, Donna Karolchik, and our sysadmin team.</p> <!---------------- 2003 archived news ---------------> <a name="2003"></a> <a name="121003"></a> <h2>Dec. 10, 2003 UCSC Releases alignments of the chimp draft assembly to human genome</h2> <p> UCSC has released alignments of the Nov. 2003 chimpanzee draft assembly to the Jul. 2003 human assembly in the Genome Browser. These alignments may be viewed on the <a href="../cgi-bin/hgTracks?org=Human&db=hg16&position=chr4:56214201-56291736">Human Jul. 2003</a> assembly. This release coincides with today's <a href="http://www.nhgri.nih.gov/11509418" target="_blank">announcement</a> by the National Human Genome Research Institute (NHGRI) of the first draft assembly of the chimpanzee genome.</p> <p> The set of human/chimpanzee alignments consists of a reciprocal best-in-genome net track and a chimp chain track. These alignments were generated using the blastz program developed at Pennsylvania State University and the programs blat, axtChain, chainNet, and netSyntenic developed at UCSC by Jim Kent. Research scientists should find these tracks useful for locating orthologous regions and studying genome rearrangement in the two species.</p> <p> For more information about the alignment tracks, refer to the track description pages. The tables may be downloaded from the Genome Browser FTP server's -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg16/database/">hg16 database directory</a>. The +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg16/database/">hg16 database directory</a>. The chimp sequence and alignment data are downloadable from the -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg16/vsPt0/">hg16 human/chimp alignments +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg16/vsPt0/">hg16 human/chimp alignments directory</a>.</p> <p> The chimp sequence used in these alignments was obtained from the Nov. 13, 2003 Arachne assembly. We'd like to thank NHGRI, the Eli & Edythe L. Broad Institute at MIT/Harvard, and Washington University School of Medicine for providing this sequence, and LaDeana Hillier, Washington University School of Medicine, and the Whitehead Institute for their work on the alignments. We'd also like to acknowledge the members of the UCSC team who contributed to the release of these alignments in the Genome Browser: Jim Kent, Kate Rosenbloom, Heather Trumbower, and Donna Karolchik.</p> <a name="112403"></a> <h2>Nov. 24, 2003 Genome Browser released for mouse assembly NCBI Build 32</h2> <p> We have released a Genome Browser and Blat server for the latest mouse genome assembly, NCBI Build 32 (UCSC v. mm4). Build 32 is a composite assembly in which chromosomes were assembled by two slightly different algorithms depending on the available mapping data. Chromosomes 2, 4, 5, 7, 11, 15, 18, 19, X, and Y were assembled using a clone-based tiling path file (TPF) provided by the Mouse Genome Sequencing Consortium (MGSC), with whole genome shotgun sequence used to fill gaps when necessary. The remaining chromosomes were assembled using the MGSCv3 whole genome shotgun assembly as the TPF and merging High Throughput Genomic Sequence (HTGS) as needed. The UCSC mm4 assembly contains only the reference strain C57BL/6J.</p> <p> Build 32 includes 2.6 gigabases of sequence, 1.2 Gb of which is finished. We estimate that 90-96 percent of the mouse genome is present in the assembly. For more information about this version, see the NCBI <a href="https://www.ncbi.nlm.nih.gov/genome/seq/NCBIContigInfo.html" target="_blank">assembly notes</a> and <a href="https://www.ncbi.nlm.nih.gov/mapview/stats/BuildStats.cgi?taxid=10090&build=32&ver=1" target="_blank">Build 32 statistics</a>.</p> <p> The mm4 sequence and annotation data may be downloaded from the UCSC Genome Browser -<a href="http://hgdownload.soe.ucsc.edu/downloads.html#mouse">downloads server</a>.</p> +<a href="http://hgdownload.gi.ucsc.edu/downloads.html#mouse">downloads server</a>.</p> <p> We'd like to thank the Deanna Church, Richa Agrawala, and the Mouse Genome Sequencing Consortium for this assembly. We'd also like to acknowledge the work of the UCSC mm4 team: Hiram Clawson (lead), Terry Furey, Kate Rosenbloom, Heather Trumbower, Bob Kuhn and Donna Karolchik, and our systems administrators Patrick Gavin, Jorge Garcia and Paul Tatarsky.</p> <a name="103103"></a> <h2>Oct. 31, 2003 <em>D. melanogaster</em> assembly added to Genome Browser</h2> <p> We have added the <em>Drosophila melanogaster</em> (fruitfly) assembly to the growing collection of genomes available in the UCSC Genome Browser and Blat servers. Release 3.1 (Jan. 2003) of the <em>Drosophila</em> annotated genome sequence was provided by the <a href="http://www.fruitfly.org/" target="_blank">Berkeley Drosophila Genome Project</a> (BDGP). The 116.8 Mb euchromatic sequence - which is virtually gap-free and of high accuracy - contains six euchromatic chromosome arms represented by 13 scaffolds with a total of 37 sequence gaps. The sequence quality of this release has an estimated error rate of less than one in 100,000 base pairs in the unique portion of the sequence, and less than one in 10,000 base pairs in the repetitive portion. The Release 3.1 sequence was reannotated using the <a href="http://www.fruitfly.org/annot/apollo/" target="_blank">Apollo Genome Annotation and Curation Tool</a>. We also provide data comparing the genome of <em>D. melanogaster</em> with that of <em>D. pseudoobscura</em>.</p> <p> The fruitfly, one of the first organisms to be used in systematic scientific investigations, has been the subject of intensive study in genetics for nearly a century and remains a major model organism in biomedical research, population biology and evolution. We are pleased to add the fruitfly to the roster of assemblies available on our site.</p> <p> Downloads of the <em>Drosophila</em> data and annotations may be obtained from the UCSC Genome -Browser <a href ="ftp://hgdownload.soe.ucsc.edu/goldenPath/dm1">ftp site</a>.</p> +Browser <a href ="ftp://hgdownload.gi.ucsc.edu/goldenPath/dm1">ftp site</a>.</p> <p> We'd like to thank BDGP and the <a href = "http://flybase.bio.indiana.edu">Flybase</a> Consortium (<a href="http://www.harvard.edu/" target="_blank">Harvard University</a>, <a href="http://www.cam.ac.uk/" target="_blank">University of Cambridge</a>, <a href="http://www.iub.edu/" target="_blank">Indiana University</a>, the <a href="http://www.berkeley.edu/" target="_blank">University of California, Berkeley</a> and the <a href="http://www.ebi.ac.uk/index.html" target="_blank">European Bioinformatics Institute</a> (EBI)) for providing the sequence, assembly, and analysis of this genome. We'd also like to acknowledge the members of the UCSC Genome Bioinformatics group who contributed to this release: Angie Hinrichs (lead engineer), Heather Trumbower, Robert Kuhn, Donna Karolchik, and Jim Kent and the system administrators Jorge Garcia, Patrick Gavin and Paul Tatarsky.</p> <a name="101703b"></a> <h2>Oct. 17, 2003 mRNA, RefSeq and EST data now updated incrementally for several assemblies</h2> @@ -20785,31 +20785,31 @@ This assembly was constructed with the JGI assembler, JAZZ, from paired end sequencing reads produced by JGI and IMCB, at JGI, Myriad Genetics, and Celera Genomics, resulting in a sequence coverage of 5.7X. All reads are plasmid, cosmid, or BAC end sequences, with the predominant coverage derived from 2 Kb insert plasmids. This assembly contains 20,379 scaffolds totaling 319 million base pairs. The largest 679 scaffolds total 160 million base pairs. The Fugu genome was annotated using the Ensembl system by the Fugu informatics group at IMCB.</p> <p> The Fugu, which was one of the first vertebrate genomes to be draft-sequenced after human, serves an important role in the exploration of the human genome. In contrast to other vertebrates that have been sequenced, the intergenic and intron regions of the Fugu are highly compressed and uncluttered with repetitive sequence, resulting in a genome that is unusually compact in size. The Fugu genome has proved useful in gene discovery and the identification and characterization of gene regulatory elements in other genomes.</p> <p> Bulk downloads of the Fugu sequence and annotation data are available via FTP at -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/fr1">ftp://hgdownload.soe.ucsc.edu/goldenPath/fr1</a> +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/fr1">ftp://hgdownload.gi.ucsc.edu/goldenPath/fr1</a> or through the Downloads link on the Genome Browser home page. We recommend that FTP be used rather than HTML for the download of large or multiple files.</p> <p> We'd like to thank JGI and the other members of the International Fugu Genome Consortium, including IMCB, the UK Human Genome Mapping Project (Hinxton), the Molecular Sciences Institute (Berkeley) and the Institute for Systems Biology (Seattle), for providing the sequence, assembly, and analysis of this genome. We'd also like to acknowledge the members of the UCSC Genome Bioinformatics group who contributed to this release: Kate Rosenbloom (lead engineer), Heather Trumbower, Robert Kuhn, Donna Karolchik, and Jim Kent.</p> <a name="081303"></a> <h2>Aug. 13, 2003 NISC Comparative Sequencing Program regions released in Genome Browser</h2> <p> The UCSC Genome Bioinformatics group has released a browser and blat server on the first of more @@ -20840,89 +20840,89 @@ <p> UCSC built a customized version of the browser to display the target region for this study, allowing scientists to interactively explore the data and predictions generated by this project, contribute data of their own, and track the project as data from additional species are generated. In addition to the browser, the UCSC team also contributed to the analytical portion of the study. Mathieu Blanchette identified the regions that are most highly conserved among species. Adam Siepel performed the phylogenetic analysis of rates of substitution. The UCSC team worked with Arian Smit to obtain definitive evidence that rodents branched off from the common ancestor later than carnivores and artiodactyls.</p> <p> For more information on the NISC study, see the <em>Science Daily</em> <a href="http://www.sciencedaily.com/releases/2003/08/030814072241.htm" target="_blank">press release</a>. Flat files of the assembled sequence and annotations may be obtained from <a href="http://www.nisc.nih.gov/data/" target="_blank">http://www.nisc.nih.gov/data/</a> or via the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html">Downloads</a> link on the Genome Browser +<a href="http://hgdownload.gi.ucsc.edu/downloads.html">Downloads</a> link on the Genome Browser home page.</p> <p> We'd like to thank the NISC Comparative Sequencing Program team for providing the data and comparative analysis for this Genome Browser release. Special thanks go to Elliott Margulies at NHGRI for serving as the main liaison between NHGRI and UCSC, and for contributing several annotation tracks to the browser. We'd also like to acknowledge the efforts of the many faculty, grad students, and staff members of the UCSC Genome Bioinformatics group who contributed to the research effort and browser development for this project.</p> <a name="080803"></a> <h2>Aug. 8, 2003 New human genome reference sequence now available in Genome Browser</h2> <p> The latest human genome reference sequence (NCBI Build 34, Jul. 2003) is now available as database hg16 in the UCSC Genome Browser and blat server.</p> <p> There are 2,843,433,602 finished sequenced bases in the ordered and oriented portion of the assembly, which is an increase of 0.4 percent, or approximately 11 Mb, over the Build 33 assembly. Of particular note in this release is the addition of the pseudoautosomal regions of the Y chromosome. This sequence was taken from the corresponding regions in the X chromosome and is an exact duplication of that sequence.</p> <p> Some sequence joins between adjacent clones in this assembly could not be computationally validated because the clones originated from different haplotypes and contained polymorphisms in the overlapping sequence, or the overlap was too small to be to be reliable. In these instances, the sequencing center responsible for the particular chromosome has provided data to support the join in the form of an electronic certificate. The Build 34 certificates may be reviewed <a href="certificates/certificate_hg16.html">here</a>.</p> <p> Bulk downloads of the data are available via FTP at -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg16">ftp://hgdownload.soe.ucsc.edu/goldenPath/hg16</a> -or through the <a href="http://hgdownload.soe.ucsc.edu/downloads.html">Downloads</a> link. We +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg16">ftp://hgdownload.gi.ucsc.edu/goldenPath/hg16</a> +or through the <a href="http://hgdownload.gi.ucsc.edu/downloads.html">Downloads</a> link. We recommend that FTP be used rather than HTML for the download of large or multiple files.</p> <p> We'd like to thank NCBI and the International Human Genome Sequencing Consortium for furnishing the data, and the UCSC team members who contributed to this release: Terry Furey, Hiram Clawson, Heather Trumbower, Mark Diekhans, Robert Baertsch, Donna Karolchik, Jim Kent and our sysadmin team Patrick Gavin, Jorge Garcia, and Paul Tatarsky.</p> <h2>Jul. 14, 2003 Rat genome v.3.1 added to Genome Browser</h2> <p> The UCSC Genome Bioinformatics Group has released a browser and BLAT server on the v. 3.1 rat genome assembly from the Rat Genome Sequencing Consortium. This assembly (UCSC version rn3, June 2003) was produced by the Atlas group at <a href="http://hgsc.bcm.tmc.edu/projects/rat/" target="_blank">Baylor Human Genome Sequencing Center</a> (HGSC). This assembly is a minor update to the 3.0 release. Sequence changes affect only chromosomes 7 and X. No additional assembly releases are planned prior to the publication of the rat genome analysis papers.</p> <p> The 3.x assemblies reflect several sequence additions and software improvements over the previous 2.x assemblies, including the sequencing of over 1100 new BACs to cover gaps, an improved marker set from the Medical College of Wisconsin, a new FPC map from the BC Genome Sciences Centre, and improved linking of bactigs. For detailed information and statistics about the 3.x assemblies, see the Baylor HGSC <a href="ftp://ftp.hgsc.bcm.tmc.edu/pub/analysis/rat/README" target="_blank">README</a>.</p> <p> Downloads of the rat sequence and annotation data are available at -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/rnJun2003/" -target="_blank"> ftp://hgdownload.soe.ucsc.edu/goldenPath/rnJun2003/</a> or via the Downloads link +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/rnJun2003/" +target="_blank"> ftp://hgdownload.gi.ucsc.edu/goldenPath/rnJun2003/</a> or via the Downloads link on this page. These data are made available with <a href="credits.html#rat_use">specific conditions for use</a>.</p> <p> We'd like to thank the Rat Genome Sequencing Consortium and Baylor HGSC for providing this assembly, collaborators from other institutions who have contributed annotations, and Arian Smit for updating RepeatMasker for this release. We'd also like to acknowledge the contributions of several individuals at UCSC, including Hiram Clawson, Heather Trumbower, Robert Kuhn, Yontao Lu, Terry Furey, Mark Diekhans, Robert Baertsch, Donna Karolchik, Jim Kent, and our sysadmin team Jorge Garcia, Patrick Gavin, and Paul Tatarsky.</p> <h2>Jun. 24, 2003 Genome Browsers released for <em>C. elegans</em> and <em>C. briggsae</em></h2> <p> UCSC has just released browsers and blat servers for 2 worms: C. elegans version WS100 (May 2003) and C. briggsae version cb25.agp8 (Jul. 2002). The browsers are based on sequence obtained from @@ -20933,34 +20933,34 @@ fully sequenced genome. In contrast, the whole genome shotgun assembly of the C. briggsae genome is estimated to have achieved 98% coverage. Draft chromosome sequences are not available for C. briggsae, due to the lack of dense chromosomal maps that allow assignment of ultracontigs to chromosomal locations. As a result, all data in the C. briggsae browser maps to chrUn.</p> <p> Both worms played a significant role in the early history of the UCSC Genome Browser. The browser code originated with a C script that displayed a splicing diagram for a gene prediction from C. elegans. Tracks for mRNA alignments and for homology with C. briggsae were added, and the tool morphed into the precursor of the Genome Browser, the "Intronerator" (Kent, WJ and Zahler, AM (2000). <a href="http://nar.oupjournals.org/cgi/content/abstract/28/1/91?ijkey=155fc1582751ebf7b01072beb40325b1d0682fdc&keytype2=tf_ipsecsha" target="_blank">The intronerator: Exploring introns and alternative splicing in C. elegans</a>. <em>Nucleic Acids Res.</em> 28: 91-93).</p> <p> Downloads of the C. elegans sequence and annotation data are available at -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/ceMay2003/" -target="_blank"> ftp://hgdownload.soe.ucsc.edu/goldenPath/ceMay2003/</a>; C. briggsae downloads can -be found at <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/cbJul2002/" -target="_blank">ftp://hgdownload.soe.ucsc.edu/goldenPath/cbJul2002/</a>. Both genomes can also be +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/ceMay2003/" +target="_blank"> ftp://hgdownload.gi.ucsc.edu/goldenPath/ceMay2003/</a>; C. briggsae downloads can +be found at <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/cbJul2002/" +target="_blank">ftp://hgdownload.gi.ucsc.edu/goldenPath/cbJul2002/</a>. Both genomes can also be downloaded via the Downloads link on this page.</p> <p> We'd like to thank the <a href="http://genome.wustl.edu/" target="_blank">Genome Sequencing Center at Washington University in St. Louis</a> and the <a href="http://www.sanger.ac.uk/" target="_blank">Sanger Institute</a> for their collaborative work in sequencing the C. elegans and C. briggsae genomes. Many thanks to the <a href="http://www.wormbase.org/about/staff" target="_blank">WormBase consortium</a> for making the worm sequence publicly available. We'd also like to acknowledge several UCSC people who contributed to this release: Hiram Clawson (browser and annotation tracks engineering), Jim Kent (WABA and chaining/netting), Al Zahler (WABA), Heather Trumbower (QA and project management), and Donna Karolchik (project management and documentation).</p> <h2>Jun. 23, 2003 Genome Browser UI changes</h2> <p> You may notice that we've removed the Genome pulldown menu and genome assembly information from our @@ -20979,132 +20979,132 @@ viral mRNA and protein alignments. Of particular note are the protein structure analysis and predictions, determined by using the <a href="http://www.soe.ucsc.edu/research/compbio/sam.html" target="_blank">Sequence Alignment and Modeling (SAM) T02</a> tool. </p> <p> This browser marks a departure from our usual collection of vertebrate genomes. Its inception was inspired by one of our engineers - Angie Hinrichs - who was vacationing in New Zealand when the SARs draft assembly was initially released. Struck by the impact of SARS in that part of the world, she downloaded the sequence and built the initial tracks from a terminal at an Internet cafe! The rest of the team joined in on the grassroots effort, generating the additional annotations and SAM T02 protein analyses and predictions. Victor Solovyev chimed in with Fgenesv+ gene predictions from Softberry Inc. UCSC does not intend to provide a comprehensive collection of viral genomes in the future, but will maintain this browser as long as scientific and public interest in SARS persists.</p> <p> Downloads of the annotation data are available at -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/scApr2003/database" -target="_blank">ftp://hgdownload.soe.ucsc.edu/goldenPath/scApr2003/database</a> or via the Downloads +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/scApr2003/database" +target="_blank">ftp://hgdownload.gi.ucsc.edu/goldenPath/scApr2003/database</a> or via the Downloads link on this page.</p> <p> We'd like to thank everyone who worked on this release, including Angie Hinrichs, Robert Baertsch, Fan Hsu, Matt Schwartz, Heather Trumbower, Jim Kent, Kevin Karplus, Donna Karolchik, Brian Raney, Hiram Clawson, Kate Rosenbloom, Victor Solovyev, and our extremely dedicated systems administrators Paul Tatarsky, Patrick Gavin, and Jorge Garcia.</p> <h2>Apr. 21, 2003 Chromosome 8 data corrected for April 2003 human assembly</h2> <p> The file that we originally used to build the agp files for the Apr. 2003 human release (Build 33) erroneously contained 2 contigs on chromosome 8 that were listed twice: NT_078037, NT_008183. We've received a corrected version and have updated the following files on our website: contigAgp.zip, chromAgp.zip, liftAll.zip. You can obtain the newer versions of these files from our ftp site at -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/10april2003/bigZips/"> -ftp://hgdownload.soe.ucsc.edu/goldenPath/10april2003/bigZips/</a>.</p> +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/10april2003/bigZips/"> +ftp://hgdownload.gi.ucsc.edu/goldenPath/10april2003/bigZips/</a>.</p> <h2>Apr. 14, 2003 Human Genome Project successfully completed!</h2> <p> The International Human Genome Sequencing Consortium today announced the successful completion of the Human Genome Project. The most significant outcome of this project is the reference sequence of the human genome. The sequencing of the 3 billion letters of DNA in the human genome - which many consider to be one of the most ambitious scientific undertakings in history - was completed 2 years ahead of schedule and at substantially less cost than original estimates. The reference sequence will serve as a new foundation for research in the fields of medicine and human biology.</p> <p> In conjunction with this announcement, the UCSC Genome Bioinformatics group is proud to release a genome browser and BLAT server on the reference sequence (NCBI Build 33), along with bulk downloads of the sequence and annotation data. The initial browser provides a preliminary set of annotations that will be expanded in coming weeks. Bulk downloads of the data are available via FTP at -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/10april2003">ftp://hgdownload.soe.ucsc.edu/goldenPath/10april2003</a> -or through the <a href="http://hgdownload.soe.ucsc.edu/downloads.html">Downloads</a> link on this +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/10april2003">ftp://hgdownload.gi.ucsc.edu/goldenPath/10april2003</a> +or through the <a href="http://hgdownload.gi.ucsc.edu/downloads.html">Downloads</a> link on this page. We recommend that FTP be used rather than HTML for the download of large or multiple files.</p> <p> The reference sequence covers about 99 percent of the human genome's gene-containing regions, and has been sequenced to an accuracy of 99.99 percent. The missing portions are essentially contained in less than 400 defined gaps that represent DNA regions with unusual structures that can't be reliably sequenced using current technology. The average DNA letter now lies within a stretch of approximately 27,332,000 base pairs of uninterrupted sequence!</p> <p> Chromosomal sequences for this release were assembled by the International Human Genome Sequencing Consortium sequencing centers and verified by NCBI and UCSC. In some cases, sequence joins between adjacent clones could not be computationally validated, e.g. due to polymorphisms in the overlapping sequence. In situations like this, supporting evidence for the join has been provided by the sequencing center responsible for that particular chromosome. The <a href="certificate.html">Non-standard Join Certificates</a> table displays this information. The annotations on the UCSC website have been provided by UCSC and collaborators worldwide. See the <a href="credits.html">Credits</a> page for a detailed list of organizations and individuals who contributed to this release.</p> <p> We'd like to congratulate the many people worldwide who have worked on the Human Genome Project for this landmark achievement. We'd also like to acknowledge the UCSC Genome Browser project team who worked many long hours to ensure that the genome browser and sequence data were released on time for this announcement: David Haussler, Jim Kent, Terry Furey, Matt Schwartz, Heather Trumbower, Angie Hinrichs, Fan Hsu, Donna Karolchik, Jorge Garcia, Patrick Gavin, Chuck Sugnet, Yontao Lu, Mark Diekhans, Ryan Weber, Robert Baertsch, Krishna Roskin, and the many other students in the UCSC Genome Bioinformatics group.</p> <h2>Apr. 2, 2003 Human assembly hg10 and mouse assembly mm1 archived</h2> <p> The Dec. 2001 Human assembly (hg10) and the Nov. 2001 Mouse assembly (mm1) have been moved to the archives. They are no longer viewable in the main browser, but can still be downloaded from the -<a href="http://hgdownload.soe.edu">downloads server</a>.</p> +<a href="http://hgdownload.gi.edu">downloads server</a>.</p> <h2>Mar. 26, 2003 New rat assembly released in Genome Browser</h2> <p> We've added an updated rat assembly to our site: Rat Jan 2003 (rn2). This corresponds to the Version 2.1 Jan 2003 Update of the rat genome assembly, produced by the Atlas group at Baylor HGSC as part of the Rat Genome Sequencing Consortium.</p> <p> This update corrects duplications that were assembly artifacts in the previous version and improves the linking of bactigs to create larger "ultrabactigs". Compared with the previous rat assembly, sequence mapped to specific chromosomal coordinates is reduced by about 1.6 percent. Loosely mapped and unmapped sequence is reduced by 17 percent. For more details and statistics on the Jan. 2003 assembly, see the Baylor HGSC <a href="ftp://rat-ftp.hgsc.bcm.tmc.edu/pub/analysis/rat/README">README</a> for this release.</p> <p> UCSC has released a Genome Browser and BLAT server for this assembly update. The initial <a href="../cgi-bin/hgTracks?db=rn2"> browser</a> contains 16 annotation tracks, with more to follow in coming weeks. Sequence downloads are currently available at -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/rnJan2003/" -target="_blank">ftp://hgdownload.soe.ucsc.edu/goldenPath/rnJan2003/</a> or via the Downloads link on +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/rnJan2003/" +target="_blank">ftp://hgdownload.gi.ucsc.edu/goldenPath/rnJan2003/</a> or via the Downloads link on this page. A complete set of database downloads will be available at the beginning of next week. This data contains <a href="credits.html#rat_use">specific conditions for use</a>.</p> <p> Thanks to the Atlas group at Baylor HGSC, the Rat Genome Sequencing Consortium, the UCSC Genome Bioinformatics group, and contributors worldwide for making this release available.</p> <h2>Mar. 13, 2003 Updated mouse genome assembly now available</h2> <p> We're happy to announce an update to the mouse genome sequence. This new version (Mouse Feb. 2003) includes 705 megabases of finished sequence, compared to 96 megabases of finished sequence in the previous assembly. Many people in the Mouse Genome Sequencing Consortium contributed to this update. The Sanger Institute in particular contributed a large amount of finished sequence. Richa Agarwala, Deanna Church, and coworkers at NCBI layered the finished clones on top of the Arachne whole genome shotgun assembly. Arian Smit constructed a new RepeatMasker library.</p> <p> UCSC has released a Genome Browser and BLAT server for the Feb. 2003 Mouse genome. The initial <a href="../cgi-bin/hgTracks?db=mm3"> browser</a> contains 14 annotation tracks, with more to follow in coming weeks. Sequence downloads are currently available at -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/mmFeb2003/" -target="_blank">ftp://hgdownload.soe.ucsc.edu/goldenPath/mmFeb2003/</a> or via the Downloads link on +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/mmFeb2003/" +target="_blank">ftp://hgdownload.gi.ucsc.edu/goldenPath/mmFeb2003/</a> or via the Downloads link on this page. Database downloads will be available at the beginning of next week.</p> <p> Thanks to everybody at UCSC and around the world that contributed to this release!</p> <h2>Feb. 5, 2003 Enhanced version of Genome Browser released</h2> <p> We're proud to announce the release of version 17 of the UCSC Genome Browser. This version contains powerful new features, numerous improvements to the annotation track display, additional annotation tracks, and a number of bug fixes. In this release cycle, we've also introduced an enhanced QA process that formalizes our testing and verification of the Genome Browser software and the data displayed in the browser.</p> <p> <strong>New functionality in v.17:</strong><br> -- Numerous enhancements to the table browser that allow the user to conduct more complex and specific searches. New features include support for intersections of tracks, a new summary @@ -21173,87 +21173,87 @@ hg13). This assembly was produced at NCBI based on sequence information submitted into GenBank as of Nov. 14, 2002. Release notes for this assembly are available from the <a href="https://www.ncbi.nlm.nih.gov/genome/guide/human/release_notes.html" target="_blank">NCBI web site</a>. Because UCSC now obtains its assembly directly from NCBI, the UCSC Build 31 data is identical to that of NCBI and Ensembl.</p> <p> Build 31 is an excellent high-quality assembly that shows a remarkable amount of progress toward the milestone of finishing the human genome. Greater than 95% of the euchromatic region of the genome is now complete, with more than 90% of the sequence in a finished state. The number of clone contig gaps has decreased by one third from the previous assembly, and the overall number of sequenced contigs has been reduced by one half. Seven chromosomes are considered to be in a finished state: 6, 7, 13, 20, 21, 22, and Y.</p> <p> The initial release of the Build 31 Genome Browser contains 25 annotation tracks, with several more to follow in the upcoming weeks. Bulk downloads of the data are available from our FTP site at -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/14nov2002" -target="_blank">ftp://hgdownload.soe.ucsc.edu/goldenPath/14nov2002</a> or via the -<a href="http://hgdownload.soe.ucsc.edu/downloads.html">Downloads</a> link on this page.</p> +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/14nov2002" +target="_blank">ftp://hgdownload.gi.ucsc.edu/goldenPath/14nov2002</a> or via the +<a href="http://hgdownload.gi.ucsc.edu/downloads.html">Downloads</a> link on this page.</p> <p> UCSC has generated a set of high-level comparisons of the Build 31 draft sequence against various types of information (STS maps, BAC end pairs, and clone overlaps). This information, as well as statistics for Build 31, is accessible from the -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/human/chromReports/14Nov2002/" +<a href="http://hgdownload.gi.ucsc.edu/goldenPath/human/chromReports/14Nov2002/" target="_blank">Chromosome Reports</a>, -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/human/mapPlots/" +<a href="http://hgdownload.gi.ucsc.edu/goldenPath/human/mapPlots/" target="_blank">Genome Map Plots</a>, and <a href="stats.html" target="_blank">Summary Statistics</a> links in the "Technical Information about the Assembled Sequence" section below.</p> <p> We'd like to thank NCBI as well as all the people who collaborated on the data and annotations for this release.</p> <h2>Dec. 6, 2002 Rat Genome assembly now available in Genome Browser</h2> <p> We're pleased to announce the release of a UCSC Genome Browser on the Nov. 2002 rat assembly produced by the Baylor College of Medicine Rat Genome Sequencing Center and the Rat Genome Sequencing Consortium. The sequence was assembled using a hybrid approach that combines the clone by clone and whole genome shotgun methods. A new software program - ATLAS - was developed for this effort. The assembly process resulted in a 6.5-fold coverage of the rat genome, which is estimated to be approximately 2.8 Gigabases in size.</p> <p> Downloads of the rat data and annotations are available through our -ftp site at <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/rn1" target="_blank">downloads +ftp site at <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/rn1" target="_blank">downloads server</a>. This data contains <a href="credits.html#rat_use">specific conditions for use</a>. The sequence is also available from the <a href="http://www.hgsc.bcm.tmc.edu/projects/rat" target="_blank">Rat Genome Project website</a> for the Human Genome Sequencing Center at Baylor College of Medicine or from GenBank.</p> <p> We'd like to thank the Baylor team and the Rat Genome Sequencing Consortium for their collaboration on this project. See the <a href="credits.html#rat_credits">Credits page</a> for a complete list of acknowledgments. For more information on the rat genome, the assembly process, and the Rat Genome Sequencing Consortium, refer to the website for the <a href="http://www.hgsc.bcm.tmc.edu/" target="_blank">Human Genome Sequencing Center at Baylor College of Medicine</a>.</p> <h2>Dec. 5, 2002 Mouse Genome Browser released</h2> <p> The International Mouse Genome Sequencing Consortium has announced the publication of a high-quality draft sequence of the mouse genome, together with a comparative analysis of the mouse and human genomes. The results from this analysis can be found in the Mouse Genome Browser on this website. The paper appears in the Dec. 5 issue of the journal Nature at <a href="http://www.nature.com/nature/mousegenome/" target="_blank">http://www.nature.com/nature/mousegenome/</a>. The co-author list includes several members of the UCSC Genome Bioinformatics Group: CBSE Director David Haussler, Research Scientist Jim Kent and research team members Robert Baertsch, Mark Diekhans, Terrence Furey, Angie Hinrichs, Fan Hsu, Donna Karolchik, Krishna Roskin, Matt Schwartz, Charles Sugnet and Ryan Weber.</p> <h2>Oct. 29, 2002 Additional data downloads available for human assembly Jun. 2002</h2> <p> We've added several new directories of downloadable data to the Jun. 28, 2002 human genome assembly. These directories contain mouse/human alignments of the Jun. 2002 human assembly vs. the Feb. 2002 mouse assembly. You can access these directories from our -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg12/" target="_blank">downloads server</a>.</p> +<a href="http://hgdownload.gi.ucsc.edu/goldenPath/hg12/" target="_blank">downloads server</a>.</p> <p> Within the main directory <em>vsMm2</em> are 3 subdirectories that contain all the alignments (<em>axtAll</em>), alignments filtered to provide only the best alignment for any given region of the human genome (<em>axtBest</em>), and a relatively stringent subset of the axtBest alignments (<em>axtTight</em>). For more information about the format of the alignment files and the methods used to generate the alignments, consult the <em>README.txt</em> file in the vsMm2 directory. </p> <h2>Oct. 18, 2002 Enhancements in v16 Genome Browser</h2> <p> We've rolled out a new version of the Genome Browser - v.16. In addition to several bug fixes, this release contains some interesting new features.</p> <p> The Table Browser has undergone major enhancements. Users can now restrict their queries by specifying a value or range for any of the fields in a table, and by selecting which fields should be displayed in the output. The Table Browser also provides the ability to do a free-form SQL query @@ -21302,175 +21302,175 @@ assembly, we've added Gene Bounds, UniGene, CpG Islands, Nonhuman mRNA & EST, SNPs, NC160, and GNF Ratio. On the Apr. 2002 assembly we've added a Fgenesh++ Genes track, and have also updated the RepeatMasker track. The Dec. 2001 release now includes a Sanger 22 track.</p> <p> On the mouse genome, we have 2 new tracks for the Feb. 2002 assembly: TIGR Gene Index and RNA Genes.</p> <h2>Aug. 6, 2002 Error with six chromosome 3 contigs in human assembly hg12</h2> <p> We have fixed an error with six of the chr3 contigs in the bigZips/contigAgp.zip file. The following .agp files were corrected: NT_005684.agp, NT_005663.agp, NT_022554.agp, NT_022459.agp, NT_006031.agp, and NT_022419.agp. The chr3.agp file in bigZips/chromAgp.zip was also modified. This change does not affect the .gl files, the .fa files, the lift files, or the annotations. Alignments made on the previous version of chr3 are still good. Updated versions of the contigAgp.zip and chromAgp.zip files were uploaded to our site today. You can download the new versions via ftp from -our <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg12" target="_blank">downloads +our <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg12" target="_blank">downloads server</a>.</p> <h2>Aug. 2, 2002 New RepeatMasker track available for human assembly hg12</h2> <p> The problems with the Jun. 2002 Build 30 (hg12) RepeatMasker track have been resolved. The new RepeatMasker track, along with regenerated Fish Blat and Genscan tracks, are now available in the Browser and through our Downloads link. We've also added a few new annotation tracks for the Jun. 2002 release, and will be adding more over the next 2 weeks.</p> <p> The latest Genome Browser has 2 new features. We've added filter functionality to the Table Browser, accessible via the Filter Fields button on the Table Browser main page. Also, some of the Dec. 2001 human genome tracks (eg. RefSeq Genes) now have a Comparative Sequence link from the details page that shows annotated codons and translated protein with alignment to the mouse genome.</p> <h2>Jul. 27, 2002 Problems with repeat-masking on human assembly hg12</h2> <p> We've experienced some RepeatMasker problems on Build 30 and are rerunning it. This will directly affect the RepeatMasker track and the masking of the fasta files. The Fish Blat and Genscan tracks may also change slightly once we're redone this. The EST, mRNA, and RefSeq tracks should not be affected. We will also post a new RepeatMasker track for Build 29 (see news item below) as soon as the Build 30 tracks are completed. We apologize for any rework this may cause.</p> <h2>Jul. 26, 2002 Bulk data downloads now available for human assembly hg12</h2> <p> Bulk downloads of the Jun. 2002 Build 30 human genome assembly (hg12) are now available from the -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg12/" target="_blank">downloads server</a>. This +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg12/" target="_blank">downloads server</a>. This initial release of the annotation database download contains a limited set of tables. Additional files will be available for download next week.</p> <h2>Jul. 24, 2002 Human assembly hg12 blat server available</h2> <p> The BLAT server and the coordinates conversion feature for human genome assembly Build 30 (hg12) are now functional.</p> <h2>Jul. 23, 2002 Pre-release of human draft assembly Build 30 in Genome Browser</h2> <p> We're pleased to announce the pre-release of a browser for human genome assembly Build 30 from NCBI (UCSC version hg12). This assembly was produced at NCBI based on sequence information submitted into GenBank as of Jun. 28, 2002. Build 30 release notes and statistics will soon be available from the <a href="https://www.ncbi.nlm.nih.gov/" target="_blank">NCBI web site</a>.</p> <p> Build 30 is an excellent high-quality assembly. It contains nearly 87% finished sequence, and 94%-97% coverage. The sequence coverage of this build is much higher than in previous releases, and there is a high level of correspondence between the sequence and the map. Currently, the human genome project appears to be on track to achieve the goal of finishing at least 95% of the human genome (using Bermuda standards) by Apr. 2003.</p> <p> UCSC has generated a set of high-level comparisons of the Build 30 draft sequence against various types of information (STS maps, BAC end pairs, and clone overlaps), accessible from the -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/human/chromReports/24Jun2002/" +<a href="http://hgdownload.gi.ucsc.edu/goldenPath/human/chromReports/24Jun2002/" target="_blank">Chromosome Reports</a> and -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/human/mapPlots/" target="_blank">Genome Map +<a href="http://hgdownload.gi.ucsc.edu/goldenPath/human/mapPlots/" target="_blank">Genome Map Plots</a> links in the "Technical Information about the Assembled Sequence" section below.</p> <p> A Blat server for Build 30 is not yet available, but should be accessible from this site later this week. Data for the mitochondrial genome and several more annotation tracks will be posted for this release as they become available. Bulk downloads of the hg12 data should be available from this site in a few days.</p> <h2>Jul. 9, 2002 Repeat-masking problems on human assembly hg11</h2> <p> We've found some problems with the repeat-masking of the Build 29 (hg11) human sequence. We're in the process of replacing the RepeatMasker track, but do not plan to redo the other tracks due to the imminent release of Build 30. Because of this, we advise that you do not use the cross-species tracks for statistical purposes.</p> <h2>Jul. 1, 2002 New look for UCSC Genome Bioinformatics home page</h2> <p> The UCSC Genome Bioinformatics home page is sporting an updated interface to accommodate the growing number of organisms supported by the UCSC Genome Browser, BLAT, and Table Browser. The list of assembly versions accessible through each of these tools can now be found on the tool's Gateway page. To reach the Gateway page, choose an organism from the dropdown list on the left sidebar of this page, then click the Browser, BLAT, or Tables link. New organisms will be added to the list in the months ahead.</p> <p> The UCSC site continues to provide a variety of bulk downloads of a genome assemblies and annotations. The list of downloadable data has been removed from the home page, but is readily available through the Downloads link on the left sidebar. The downloads list can also be accessed directly at -<a href="http://hgdownload.soe.ucsc.edu/downloads.html">http://hgdownload.soe.ucsc.edu/downloads.html</a> -or through our ftp site at <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/" -target="_blank">ftp://hgdownload.soe.ucsc.edu/goldenPath/</a>.</p> +<a href="http://hgdownload.gi.ucsc.edu/downloads.html">http://hgdownload.gi.ucsc.edu/downloads.html</a> +or through our ftp site at <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/" +target="_blank">ftp://hgdownload.gi.ucsc.edu/goldenPath/</a>.</p> <p> Several new annotation tracks have been added to our site in the past couple weeks. The Feb. 2002 mouse assembly now has tracks for BAC End pairs, Fgenesh++ gene predictions, and AltGenie gene predictions based on Affymetrix's Genie gene-finding software. New to the Apr. 2002 human assembly is the GenMapDB Clones track, which shows placements of BAC clones from the GenMapDB database based on BAC end sequencing information and confirmed using STS markers by Vivian Cheung's lab at U. Penn. We've also changed the Known Genes track name to RefSeq Genes in all assemblies.</p> <p> This release also includes an updated <a href="help/hgTracksHelp.html" target="_blank">User's Guide</a> and more detailed documentation on creating & using <a href="help/customTrack.html" target="_blank">custom annotation tracks</a>.</p> <h2>May 24, 2002 Bulk data downloads for human assembly hg11 now available</h2> <p> Bulk downloads of the April 2002 hg11 human genome assembly (NCBI Build 29) are now available from -the <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg11/" target="_blank">downloads +the <a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg11/" target="_blank">downloads server</a>.</p> <h2>May 22, 2002 Human draft assembly Build 29 released in Genome Browser</h2> <p> We've just released a browser and BLAT server on the latest Build 29 human genome assembly from NCBI (UCSC version hg11). This assembly is based on sequence information submitted into GenBank as of Apr. 5 2002. As with the Dec. 2001 (hg10) release, this assembly was produced at NCBI rather than at UCSC. Consult NCBI's Build 29 release notes and statistics for more information about this release. This assembly contains nearly 75% finished sequence. Currently, the human genome project appears to be on track to achieve the goal of finishing at least 95% of the human genome (using Bermuda standards) by Apr. 2003.</p> <p> Although the NCBI human genome assembly has been steadily improving over the past year, mapping problems still exist in the current release. Most are small, relatively local rearrangements. Larger scale problems include a rearrangement in the p-arm of Chr16 and several discrepancies in Chr17. Researchers - especially positional cloners - are strongly encouraged to use the tools provided -(<a href="http://hgdownload.soe.ucsc.edu/goldenPath/human/mapPlots/" target="_blank">comparison -plots</a>, <a href="http://hgdownload.soe.ucsc.edu/goldenPath/human/chromReports/" +(<a href="http://hgdownload.gi.ucsc.edu/goldenPath/human/mapPlots/" target="_blank">comparison +plots</a>, <a href="http://hgdownload.gi.ucsc.edu/goldenPath/human/chromReports/" target="_blank">chromosome reports</a>) to evaluate the accuracy of the assembly in specific regions of interest.</p> <p> Bulk downloads of the hg11 data should be available from this site in approximately one week. New annotation tracks will be posted as soon as they become available.</p> <h2>Apr. 24, 2002 Bulk data downloads of mouse assembly Feb. 2002 available</h2> <p> Bulk downloads of the February 2002 mouse genome assembly are now available from the -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/mm2/" target="_blank">downloads server</a>.</p> +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/mm2/" target="_blank">downloads server</a>.</p> <h2>Apr. 19, 2002 New mouse genome assembly released</h2> <p> The Feb. 2002 mouse genome assembly is now available in the browser and for BLAT searching. This assembly was produced at the Whitehead Institute using their Arachne software. We'd like to thank them and the Mouse Genome Sequencing Consortium for providing this assembly, which has <a href="credits.html#mouserestrict">specific conditions for use</a>. Bulk downloads of the data should be available in approximately one week. Coordination with mouse genome data access at <a href="http://www.ensembl.org/Mus_musculus/">Ensembl</a> and <a href="https://www.ncbi.nlm.nih.gov/genome/guide/mouse/">NCBI</a> is in progress. We'd also like to acknowledge the UCSC team that produced this release: Jim Kent, Terry Furey, Matt Schwartz, Fan Hsu, Yontao Lu, Donna Karolchik, Chuck Sugnet, and Ryan Weber.</p> <h2>Apr. 9, 2002 Bulk data downloads of mouse assembly Nov. 2001 available</h2> <p> Bulk downloads of the November 2001 mouse genome assembly are now available from the -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/mm1/" target="_blank">downloads server</a>.</p> +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/mm1/" target="_blank">downloads server</a>.</p> <h2>Apr. 2, 2002 Release of new Genome Browser version and mouse/human annotations</h2> <p> An updated version of the UCSC Genome Browser (v.11) is now available. Along with the v.11 browser, we've released several new annotation tracks on the latest human and mouse assemblies. The new Human Dec. 2001 tracks include: Mouse Synteny, Ensembl, Genscan, CpG Islands, Mouse Blat, Fish Blat, Unigene/SAGE, NCI60 Microarray, GNF Affymetrix Microarray, Rosetta Microarray, and SNPs. An STS Markers track has been added to the Mouse Nov. 2001 browser.</p> <h2> Mar. 14, 2002 Mouse draft assembly Nov. 2001 released in Genome Browser</h2> <p> The November 2001 mouse genome assembly is now available for viewing in the browser and for BLAT searching. This assembly was produced at the Sanger Center using the Phusion software developed by Jim Mullikin and Zemin Ning, and was tied to the mouse fingerprint map by Tim Hubbard. We'd like to thank them and the Mouse Genome Sequencing Consortium for providing this assembly, which has @@ -21629,38 +21629,38 @@ <h2>Oct. 12, 2001 New gene prediction tracks for Apr. and Aug. browsers</h2> <p> Several new sets of gene predictions came in this week. We now have fgenesh++ predictions for the April freeze, and Genscan and Acembly predictions for the August freeze.</p> <h2>Oct. 11, 2001 Table Browser upgraded</h2> <p> Why struggle with massive genomic file downloads when the UCSC <a href="../cgi-bin/hgTables">Table Browser</a> lets you select exactly the track data desired via a convenient web interface? Major new improvements by Krish Roskin have empowered and simplified this feature available now for the three most recent assemblies.</p> <h2>Oct. 8, 2001 Oct. 2000 assembly moved to archives</h2> <p> The October 2000 assembly has been moved to the -<a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg5/">archives</a> to make room for the August +<a href="http://hgdownload.gi.ucsc.edu/goldenPath/hg5/">archives</a> to make room for the August assembly.</p> <h2>Oct. 5, 2001 Revised Aug. 2001 assembly released</h2> <p> A revised Aug. 2001 freeze assembly is now up. The problems with flipped contigs of finished clones and high levels of sequence duplication are fixed. You can now download this assembly -<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg8/">in bulk</a> as well as browse it. +<a href="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg8/">in bulk</a> as well as browse it. Chromosome by chromosome and annotation database files will be following over the next day or two.</p> <h2>Oct. 2, 2001 Convert coordinates between different draft assemblies</h2> <p> You can now convert coordinates between different versions of the draft using a new program, hgCoordConv, written by Chuck Sugnet. hgCoordConv attempts to cut out sequences of the original draft and align them to the new draft. When aligning the sequences to the new draft hgCoordConv makes sure that the sequences are in the same order, orientation, and have the correct distances between them.</p> <p> Chuck has also implemented a SAGE/Unigene track in the browser. This track displays data from the <a href="https://www.ncbi.nlm.nih.gov/SAGE/" target="_blank">SAGEMap project at NCBI</a>. UniGene cluster sequences are displayed in the browser and colored according to their average SAGE counts over a series of experiments. Selecting one of the UniGene representative sequences displays the