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 @@
  • BRCA Variants -
    Shows single nucleotide variants (SNVs) and small insertion/deletion variants of < 50 nucleotides (indels)
  • BRCA Structural Variants -
    Shows variants <= 50 nucleotides
  • ACMG Popfreq Variants -
    Shows the provisionally-assigned ACMG evidence code for the Population Frequency group, for variants of < 50 nucleotides
  • ACMG Popfreq SVs -
    Shows the provisionally-assigned ACMG evidence code for the Population Frequency group, for variants of <= 50 nucleotides

    • -The ENIGMA BRCA1/BRCA2 specs 1.1.0 track hub contains data from the ClinGen ENIGMA BRCA1 and BRCA2 Expert Panel Specifications 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 CSpec Registry.

    Data and Downloads:

    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.

    Apr. 13, 2021    New Haploinsufficiency predictions for human (hg19)

    We are happy to announce a new haploinsufficiency predictions track for human assembly GRCh37/hg19. This track displays haploinsufficiency predictions for human genes from @@ -6370,34 +6370,34 @@

  • Scaffold count: 994
  • Total size: 2,897,824,427
  • Acknowledgments

    • Data and Downloads:

    Feb. 3, 2021    New Exome Sequencing Probesets for human (hg38/hg19)

    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:

    @@ -6486,33 +6486,33 @@
  • NCBI BioProject ID: 318403
  • NCBI BioSample ID: SAMN04851098
  • Scaffold count: 794
  • Total size: 2,343,218,756
  • Acknowledgments

    • Data and Downloads:

    Jan. 22, 2021    Updates to gnomAD variation track (GRCh37/hg19)(GRCh38/hg38)

    We are pleased to announce updates to the gnomAD Variants super-track for the hg19/GRCh37 and hg38/GRCh38 human assemblies.


    We would like to thank the publication authors Li et al and Liu et al for making these data available. We would also like to thank Jason Fernandes, COG-UK, GenBank, the GISAID Initiative, the COVID-19 Host Genetics Initiative (HGI) and their partners, as well as Rachel Liao, Juha Karjalainen, and Kumar Veerapen from the Broad Institute.

    These tracks are made possible due to the worldwide efforts of scientists, including the Genome Browser team. We will continue to provide SARS-COVID-2 resources as they become available. For the latest data, see our -preview site. Note that content on our preview server has not undergone our QA process, and is subject to change at any time.

    Dec. 23, 2020    New ClinVar Interpretations track for human (hg19/hg38)

    We are pleased to release a new track, ClinVar Interpretations, for the hg19/GRCh37 and hg38/GRCh38 human assemblies. This track can be found as part of the ClinVar Composite. It is the first track to use our bead graph display, which is a variation of our existing lollipop display.

    @@ -6771,33 +6771,33 @@

  • NCBI BioProject ID: 384558
  • NCBI BioSample ID: SAMN06841387
  • Scaffold count: 7,873
  • Total size: 2,400,934,290
  • Acknowledgments

    • Data and Downloads:

    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.

    Dec. 2, 2020    New and updated UniProt tracks for 117 assemblies

    We are pleased to announce new and updated UniProt tracks for the following assemblies:


    @@ -7141,32 +7141,32 @@ NCBI Genome ID: 52 (Mus musculus)
  • NCBI Assembly ID: 7358741
  • NCBI BioProject ID: 20689

    • For more information about the files included in the GRCm39 GenBank submission, see the GRCm39 README. The GRCm39 GenBank record provides a detailed array of statistics about this assembly. Bulk downloads of the sequence and annotation data may be obtained from the -Genome Browser FTP server or -the Downloads +Genome Browser FTP server or +the Downloads page. The annotation tracks for this browser were generated by UCSC and collaborators worldwide.

    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.

    Oct. 21, 2020    October 21st release for SARS-CoV-2 genome browser

    We are pleased to announce our fourth data release for the coronavirus genome browser. (See also our first, second, and third releases)

    @@ -7233,31 +7233,31 @@ identify selection sites of interest in SARS-CoV-2 data from GISAID.

  • Phylogenetic Tree and Variants from High-coverage Sequences in Public Databases - This track displays a phylogenetic tree inferred from SARS-CoV-2 genome sequences from GenBank, COG-UK and the China National Center for Bioinformation, and variants found in the sequences. It uses the phylogenetic tree from the sarscov2phylo 28-08-20 release, pruned to include only public sequences. Since the public sequences are unrestricted, we can offer VCF files with -sequence variants for download.
  • Spike protein receptor-binding domain (S RBD) Deep Mutational Scanning - Tracks created from this data include:

    Thanks to Robert Kuhn for production and to the Browser staff for all the features.

    Jun. 25, 2020    Vertebrate Genomes Project assembly hub update

    -We are proud to announce our first major update to the Vertebrate Genomes Project assembly hub. This is a follow up to our initial release, and expands the hub to 168 assemblies.

    With this update, we have created three additional hubs in addition to the main hub:

    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. Assembly statistics and - +href="https://hgdownload.gi.ucsc.edu/hubs/VGP/asmStats.html">Assembly statistics and + track statistics are also available for all hubs. Links to the different pages are included below:

    - - - - + + + + - - - - + + + + - - - - + + + +
    Available VGP assemblies
    Index pages: primary assemblyalternate/haplotypetrio mat/patlegacy/supersededprimary assemblyalternate/haplotypetrio mat/patlegacy/superseded
    Assembly statistics: primary assemblyalternate/haplotypetrio mat/patlegacy/supersededprimary assemblyalternate/haplotypetrio mat/patlegacy/superseded
    Track statistics: primary assemblyalternate/haplotypetrio mat/patlegacy/supersededprimary assemblyalternate/haplotypetrio mat/patlegacy/superseded

    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. -greater horseshoe bat. This page also includes information on starting a local BLAT server for the assembly.

    We would like to thank the Vertebrate Genomes Project and the Genome 10k Project 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.

    Jun. 19, 2020    Updated Self Chain track for human (GRCh38/hg38)

    We have updated the Self Chain 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 @@

    We are pleased to announce new NCBI RefSeq assembly hubs for vertebrate genomes. Currently these hubs contain 295 assemblies, encompassing most RefSeq vertebrate genomes.

    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.

    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.


    These assemblies can be found on our list of Public Hubs, or by searching for a species by NCBI accession or name directly from the Gateway page.

    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.

    May. 22, 2020    Updated GENCODE gene tracks: Human V34 (hg19/hg38) - Mouse M25 (mm10) and updated GTEx V8 gene expression track in hg38

    @@ -9202,38 +9202,38 @@

    Mar. 17, 2020    New mitochondrial sequence for human (hg19)

    We are pleased to announce the release of a patch to the hg19 assembly that will introduce a new mitochondrial sequence, chrMT, 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), NC_012920. The new chrMT is the rCRS, NC_012920. Patch sequences from GRCh37.p13 have also been added to hg19.

    More information on how patch sequences are incorporated can be found on the Patching up the Genome blog post. The blog post contains details about the new -/latest 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.

    Also, with these patches, the hg19 genome is not optimal anymore for aligners. So we added an -"analysis set" version of the hg19 genome fasta file to our -bigZips +bigZips directory, and indexes for BWA, Bowtie2, and Hisat2.

    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.

    Feb. 27, 2020    New NCBI RefSeq Select + MANE track for Human (hg38)

    We are pleased to announce a new track, RefSeq Select+MANE, for the GRCh38/hg38 human assembly. This track is a combination of NCBI transcripts with the RefSeq Select tag, as well as transcripts with the MANE Select 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.

    @@ -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:

    Data Access

    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 hg19 -and hg38, and a -shared secondary +(bigDbSnp) for hg19 +and hg38, and a +shared secondary details file which holds additional variant details.

    Additional information including visibility display, a complete list of UCSC notes, and a methods section can be found in the track description page.

    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.

    Nov. 27, 2019    New EPD TSS track for human and mouse

    We are pleased to announce the release of the new EPDnew Promoters track for human @@ -9847,75 +9847,75 @@

  • NCBI BioProject ID: 476474
  • NCBI BioSample ID: SAMN09435472
  • Scaffold count: 2,979
  • Total size: 2,971,331,530
  • Acknowledgments

    • Data and Downloads:

    Aug. 28, 2019    Vertebrate Genomes Project assembly hub

    -The UCSC Genome Browser is proud to announce its Vertebrate Genomes Project assembly hub. The Vertebrate Genomes Project (VGP) aims to generate near error-free reference genome assemblies of all 70,000 extant vertebrate species.

    -As of now, the VGP assembly hub includes 24 vertebrate assemblies. See our assembly statistics page 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:

    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 -Canada lynx or gene count and genome coverage of NCBI genes for the -platypus.

    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 -greater horseshoe bat. This page also includes information on starting a local BLAT server for the assembly.

    We would like to thank the Vertebrate Genomes Project and the Genome 10k Project 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.

    Jul. 31, 2019    New Genome Browser: Horse, equCab3 (Equus caballus)

    A genome browser is now available for the Equus caballus assembly released in Jan. 2018 by the University of Louisville (EquCab3.0). @@ -9934,33 +9934,33 @@

  • NCBI BioProject ID: 421018
  • NCBI BioSample ID: SAMN02953672
  • Scaffold count: 4,701
  • Total size: 2,506,966,135
  • Acknowledgments

    • Data and Downloads:

    Jul. 19, 2019    New GENCODE V31 gene tracks for human, hg19 and hg38

    We are pleased to announce the release of the new GENCODE Gene annotation tracks, which corresponds to the Ensembl 97 release for human assemblies, hg19/GRCh37 and hg38/GRCh38. 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:

    @@ -10006,31 +10006,31 @@

    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:

    You can read more about how these tracks were created on the track description page for the hg38/GRCh38 version of these tracks. The TransMapV4 data can still be found in our -download server.

    +download server.

    Thanks to Mark Diekhans and Lou Nassar for their work in creating and releasing these tracks.

    Jul. 9, 2019    Expanded CRISPR track released for human (hg19/GRCh37)

    We are pleased to announce the release of an expanded CRISPR Targets track for the human hg19/GRCh37 assembly. This track shows the DNA sequences targetable by CRISPR RNA guides using the Cas9 enzyme from S. pyogenes (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 CRISPOR.

    @@ -10114,37 +10114,37 @@
  • NCBI BioProject ID: 54005
  • NCBI BioSample ID: SAMN02981400
  • Scaffold count: 71,135
  • Total size: 2,959,373,024
  • Acknowledgments

    • Data and Downloads:

    Jun. 25, 2019    JSON API now available

    The UCSC Genome Browser is pleased to announce its new JavaScript Object Notation (JSON) Application Programming Interface (API). The API provides direct access to different data including annotations and sequence data for both native Genome Browser assemblies as well as hubs.

    Some functions possible with the API include: @@ -10277,33 +10277,33 @@

  • NCBI BioProject information: PRJEB21211
  • NCBI BioSample information: SAMEA104116709
  • Contig+scaffold count: 71,598
  • Total size: 2,358,908,658
  • Acknowledgments

    • Data and Downloads:

    May 21, 2019    New Genome Browser: Cat, felCat9 (Felis catus)

    A genome browser is now available for the Felis catus assembly released in November 2017 by the Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine (Felis_catus_9.0).

    About the assembly:

    Data and Downloads:

    Apr. 10, 2019    GENCODE Genes VM20 track released for mouse (GRCm38/mm10)

    We are pleased to announce the release of the GENCODE Genes VM20 track for the Mouse assembly (GRCm38/mm10). In this GENCODE Genes update, we have made the ENSMUST* IDs the default IDs and have added the GENCODE pseudogenes to the knownGene tables.

    @@ -10718,33 +10718,33 @@
  • NCBI BioProject information: 13342
  • NCBI BioSample information: SAMN02981218
  • Contig+scaffold count: 1928
  • Total size: 1,065,365,425
  • Acknowledgments

    • Data and Downloads:

    Nov. 19, 2018    New Genome Browser: Orangutan, ponAbe3 (Pongo pygmaeus abelii )

    A genome browser is now available for the Pongo pygmaeus abelii assembly released in January 2018 by the University of Washington (Susie_PABv2).

    About the assembly:

    Data and Downloads:

    Nov. 16, 2018    GENCODE Genes v29 track released for human (GRCh38/hg38)

    We are pleased to announce the release of the GENCODE Genes v29 track for the Human (GRCh38/hg38) 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.

    More details about the GENCODE Genes v29 track can be found on the GENCODE Genes track description @@ -10922,32 +10922,32 @@ anoGam3.

    Garter snake (Thamnophis_sirtalis-6.0/thaSir1)

    Bulk downloads of the sequence and annotation data may be obtained from the -Genome Browser FTP server or the -Downloads page. Please observe the +Genome Browser FTP server or the +Downloads page. Please observe the conditions of use when accessing and using these data sets. The annotation tracks for this browser were generated by UCSC and collaborators worldwide. See the Credits for a detailed list of the organizations and individuals who contributed to these releases.

    Aug. 10, 2018    New interact track type

    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 @@

  • NCBI Assembly information: 1474531 (Pmar_germline 1.0)
  • BioProject information: 357048
  • BioSample information: SAMN06131802
  • Contig+scaffold count: 36,453
  • Total size: 1,130,417,696
  • Acknowledgments

    • Data and Downloads:

    Feb. 20, 2018    New video: Visibility control in the Browser

    We have released a new video demonstrating the visibility controls in the Browser. In our Browser training workshops 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 @@

  • BioProject information: NCBI Bioproject: 169343
  • BioSample information: NCBI Biosample: SAMEA1029457
  • Contig+scaffold count: 132,340
  • Total size: 3,286,643,896
  • Acknowledgments

    • Data and Downloads:

    Dec. 13, 2017    New NCBI RefSeq Functional Elements tracks for human and mouse

    We are pleased to announce the release of a new set of functional regulatory elements for the hg38/GRCh38 and mm10/GRCm38 assemblies. NCBI is now providing RefSeq and Gene 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 @@

  • BioProject information: NCBI Bioproject: 12348
  • BioSample information: NCBI Biosample: SAMN00000117
  • Contig+scaffold count: 68,152
  • Total size: 1,440,398,454
  • Acknowledgments

    • Data and Downloads:

    Nov. 21, 2017    New NCBI RefSeq tracks for mouse, mm10

    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:

    Data and Downloads:

    Nov. 13, 2017    New genome browser: Pig, susScr11 (Sus scrofa)

    Please welcome susScr11, the 191st genome assembly in the UCSC Genome Browser. This is the third assembly in the browser for pig (Sus scrofa) .

    About the assembly:

    Data and Downloads:

    Nov. 07, 2017    New genome browser: Chinese hamster (Cricetulus griseus) ovary cell line, CHO-K1

    Please welcome criGriChoV1, the 190th genome assembly in the UCSC Genome Browser. This assembly marks the first cell line to reside in the browser; the Chinese hamster (Cricetulus griseus) ovary cell line, CHO-K1.

    About the assembly:

    Data and Downloads:

    Nov. 2, 2017    New Zebrafish assembly danRer11 available!

    A genome browser is now available for the Zebrafish (Danio rerio) assembly released in May 2017 by The Genome Reference Consortium. For more information and statistics about this assembly, see the NCBI assembly record for GRCz11. There are 20,680 contigs and 2,848 scaffolds in this assembly with a total size of 1,679,203,469 bases.

    Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser FTP -server or the Downloads +href="ftp://hgdownload.gi.ucsc.edu/goldenPath/danRer11">Genome Browser FTP +server or the Downloads page. Please observe the conditions for use when accessing and using these data sets. The annotation tracks for this browser 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.

    Oct. 27, 2017    Public European UCSC MariaDB server now available!

    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:

     mysql --user=genome --host=genome-euro-mysql.soe.ucsc.edu -A
    @@ -12079,41 +12079,41 @@

    hg19: GTEx Tissue eQTL
    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.

    These two tracks join the previously released GTEx data tracks and track hubs in the UCSC Genome Browser:

    Please see the related October 11, 2017 publication in Nature, "Genetic effects on gene expression across human tissues" for an in-depth article about these data.

    Acknowledgments to UCSC Genome Browser engineer, Kate Rosenbloom, for creating these tracks.

    Sep. 29, 2017    VAI tool can now output HGVS terms

    @@ -12298,31 +12298,31 @@ href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu.

    We would like to thank Hiram Clawson, Maximilian Haeussler, Christopher Lee, and Jairo Navarro for the development and release of these tracks.

    Jul. 14, 2017    New alternative mouse strain hub and strain-specific annotations

    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 Public Hubs or the following -page. +page.

    Along with the release of this assembly hub, a new track is available for mm10. The Mouse SNPs 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).

    Special thanks to Joel Armstrong, Ian Fiddles, and Benedict Paten for the alignment generation, as well as Thomas Keane and the Mouse Genomes Project for providing the genome assemblies. Thanks to Hiram Clawson and Jairo Navarro for the development and release of this track and hub.

    Jul. 14, 2017    New Video: Multi-Region mode for viewing discontinuous regions in the Browser

    @@ -12402,31 +12402,31 @@ how you can get boxplots of data points to show up on track item details pages? Well, look no further as we have just released support for a GTEx style barChart track format. 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 documentation for further explanation and examples.

    Along with the release of this new track format are some tools that help to create the tracks, expMatrixToBarchartBed and bedJoinTabOffset. Both utilities are free for -all use cases, and can be downloaded from our +all use cases, and can be downloaded from our directory of utilities. For more information about this new track format and helper scripts, please see the help documentation.

    Thanks to Kate Rosenbloom, Christopher Eisenhart and Christopher Lee for the development and testing of this new track format.

    Jun. 8, 2017    New command line tool for annotating variants, vai.pl

    We are pleased to announce the release of a new command-line tool for annotating variants, vai.pl. This program is similar to our web-based Variant Annotation Integrator (VAI), except it allows for bypassing @@ -12446,64 +12446,64 @@ Thanks to Angie Hinrichs and Christopher Lee for the development and testing of the program.

    Jun. 6, 2017    New genome browser available for ciona intestinalis

    A genome browser is now available for the ciona intestinalis(vase tunicate) 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 Ciona intestinalis. There are 6,381 contigs and 1,272 scaffolds in this assembly with a total size of 115,227,500 bases.

    Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -FTP server or the -Downloads page. +FTP server or the +Downloads page. Please observe the conditions for use when accessing and using these data sets. The annotation tracks for this browser 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.

    Jun. 2, 2017    New default tracks for human and mouse assemblies

    We have made several changes to the sets of default tracks for some of our human and mouse assemblies. The GTEx Gene Expression track is now part of the set of default tracks for both human genome assemblies hg38 and hg19. In addition, we have added the DGV Struct Var 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 60-way Vertebrate Conservation track to its set of default tracks.

    May 16, 2017    New genome browser available for golden eagle

    A genome browser is now available for the golden eagle (Aquila chrysaetos canadensis) assembly released in October 2014 by Washington University. For more information and statistics about this assembly, see the NCBI assembly record for Aquila_chrysaetos-1.0.2. There are 17,032 contigs and 1,142 scaffolds in this assembly with a total size of 1,192,743,076 bases.

    Bulk downloads of the sequence and annotation data may be obtained from the Genome Browser -FTP server or the -Downloads page. +FTP server or the +Downloads page. Please observe the conditions for use when accessing and using these data sets. The annotation tracks for this browser 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.

    May 15, 2017    New TransMap annotation tracks released

    We are pleased to announce the release of a new set of TransMap V4 tracks for nearly 70 different assemblies.

    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:

    See the Wellcome Trust Sanger Institute MHC Haplotype Project web site for additional information on the chr6 alternate haplotype assemblies.

    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.

    For further information on NCBI Build 36.1, see the NCBI Build 36.1 release notes.

    Bulk downloads of the data are available from the UCSC downloads server via -ftp or -http. We recommend +ftp or +http. We recommend that you use ftp or rsync for downloading large or multiple files.

    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.

    Mar. 6, 2006    Purple Sea Urchin genome assembly available in Genome Browser

    The Apr. 2005 release of the Purple Sea Urchin genome (Strongylocentrotus purpuratus) 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.

    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.

    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 (e.g. 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.

    More assembly details can be found in the Spur_0.5 README file and on the BCM HGSC Sea Urchin Genome Project web page.

    Bulk downloads of the sequence and annotation data are available via the Genome Browser -FTP server or the -Downloads page. These data have +FTP server or the +Downloads page. These data have specific conditions for use. The strPur1 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.

    Feb. 27, 2006    Upcoming Genome Browser seminars in Texas, Florida and Washington, DC

    The UCSC Bioinformatics Group announces four regional seminars and hands-on computer workshops on the UCSC Genome Browser, presented by OpenHelix: