be4311c07e14feb728abc6425ee606ffaa611a58 markd Fri Jan 22 06:46:58 2021 -0800 merge with master diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 13d64f3..f89d609 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -37,33 +37,292 @@ <li><a href="#2006">2006 News</a></li> </ul> </div> <div class="col-sm-3"> <ul> <li><a href="#2005">2005 News</a></li> <li><a href="#2004">2004 News</a></li> <li><a href="#2003">2003 News</a></li> <li><a href="#2002">2002 News</a></li> <li><a href="#2001">2001 News</a></li> </ul> </div> </div> </div> +<!-- ============= 2021 archived news ============= --> +<a name="2021"></a> + +<a name="011321"></a> +<h2>Jan. 13, 2020 New GENCODE gene tracks: Human V35/V36 (hg19/hg38)</h2> +<p> +We are pleased to announce new GENCODE Gene annotation tracks, which correspond +to <a href="http://www.ensembl.info/2020/08/20/ensembl-101-has-been-released/" +target="_blank">Ensembl 101</a> and <a target="_blank" +href="https://www.ensembl.info/2020/11/30/ensembl-102-has-been-released/">Ensembl 102</a>, +for the <a target="_blank" +href="../../cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgEncodeGencodeV36lift37">hg19/GRCh37</a> and +<a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38c=chr1&g=wgEncodeGencodeSuper">hg38/GRCh38</a> +human assemblies. The annotations were mapped to hg38 and then back-mapped +to the hg19 assembly. All gene sets contain the following tracks:</p> +<ul> + <li>Basic - a subset of the <em>Comprehensive set</em>.</li> + <li>Comprehensive - all GENCODE coding and non-coding transcript annotations, including + polymorphic pseudogenes. This includes both manual and automatic annotations.</li> + <li>Pseudogenes - all annotations except polymorphic pseudogenes.</li></ul> +<p> +The hg38 annotations also include the following tracks not available on hg19: +</p> +<ul> + <li>2-way Pseudogenes - pseudogenes predicted by both the Yale Pseudopipe and UCSC + Retrofinder pipelines.</li> + <li>PolyA - polyA signals and sites manually annotated on the genome based on transcribed + evidence (ESTs and cDNAs) of 3' end of transcripts containing at least 3 A's not matching the + genome.</li></ul> +<p> +Details on each release can be found on the <a target="_blank" +href="https://www.gencodegenes.org/">GENCODE site</a>. This includes <a target="_blank" +href="https://www.gencodegenes.org/human/stats.html">statistics on each release</a>. +<p>We would like to thank the <a target="_blank" +href="https://www.gencodegenes.org/pages/gencode.html">GENCODE project</a> for providing these +annotations. We would also like to thank Mark Diekhans and Lou Nassar for the development and +release of these data.</p> + +<a name="010821"></a> +<h2>Jan. 8, 2020 January 8th SARS-CoV-2 update</h2> +<p> +We are pleased to start the year with our fifth 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>, <a href="#080720">third</a>, +and <a href="#102120">fourth</a> releases)</p> + +<p> +This update includes an updated track as well as three new tracks for +the <a href="/cgi-bin/hgTracks?db=wuhCor1" +target="_blank">coronavirus genome browser</a>, and a track for the <a +href="/cgi-bin/hgTracks?db=hg19" target="_blank">hg19/GRCh37</a> and <a +href="/cgi-bin/hgTracks?db=hg38" target="_blank">hg38/GRCh38</a> human assemblies. Worth note is +the <a href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=lineageB_1_1_7_US" +target="_blank">B.1.1.7 in USA</a> +track which shows substitution and deletion variants in the <b>B.1.1.7 lineage</b>, known for its +rapid spread in England in November and December 2020, alongside the first nine genome +sequences in the United States that were assigned to the lineage.</p> + +<p> +We have also updated our <a target="_blank" href="/cgi-bin/hgPhyloPlace">web interface</a> +to <a target="_blank" href="https://github.com/yatisht/usher">UShER</a>, a tool for +placing new SARS-CoV-2 sequences in a global phylogenetic tree, +to include <a target="_blank" href="https://www.cogconsortium.uk/data/">COG-UK</a> +sequences available as of Dec. 30, 2020 including thousands of new sequences in +the B.1.1.7 lineage.</p> + +<p> +Clicking on any of the track titles below will lead to the track description page, +which includes additional information and allows for configuration of various display options.</p> +<p> +This release includes the following tracks:<br><br></p> + +<ul><li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=lineageB_1_1_7_US"> +B.1.1.7 in USA</a> - This track shows single-nucleotide variants +and deletions from the SARS-CoV-2 reference genome in the B.1.1.7 consensus sequence +and the first nine genome sequences in the United States that were assigned to B.1.1.7. +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=escape"> +Antibody escape</a> - This track contains mutations +in the Spike protein that attenuate monoclonal and serum antibody neutralization.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=pbmShanghai"> +S Antib Pept Array</a> - This track shows intensities of a microarray spotted +with short peptides derived from the S protein. Sera from both convalescent COVID-19 +and control patients were screened on the peptide microarray for both IgG and IgM responses.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chr1&g=covidHgiGwasR4Pval"> +COVID GWAS v4 (hg38</a>, <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg19&c=chr1&g=covidHgiGwasR4Pval"> +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/" +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" +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> +The <b>ClinVar Interpretations track</b> displays the genomic positions of individual variant +submissions and interpretations of the clinical significance, as well as their relationship +to disease in the ClinVar database. As seen on the image below, the variants are classified into +six categories each on a separate horizontal line:</p> + +<p class="text-center"> + <img class='text-center' src="../images/clinVarInterp.png" width='100%' +alt="ClinVar Interpretations track with bead graph display."> +</p> + +<ul> +<li><font color="d20000"><b>P</b> - Pathogenic</font></li> +<li><font color="d20000"><b>LP</b> - Likely Pathogenic</font></li> +<li><font color="000088"><b>VUS</b> - Variant of Unknown Significance</font></li> +<li><font color="#00d200"><b>LB</b> - Likely Benign</font></li> +<li><font color="#00d200"><b>B</b> - Benign</font></li> +<li><font color="#888"><b>OTH</b> - Others</li></font></ul> + +<p> +The size of the bead on the line represents the number of submissions at that genomic position. +The color of the beads aids to distinguish the categories further. Hovering on the track +items shows the genomic variations which start at that position and the +number of individual submissions with that classification. Additional information on the variants +can be found by clicking into the item.</p> +<p> +For more information see the <a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&c=chr10&g=clinvar">track description page</a>.</p> +<p> +We would link to thank <a target="_blank" href="https://www.ncbi.nlm.nih.gov/clinvar/">ClinVar</a> +for making these data available, as well as Brian Joseph Raney, Ana Benet Pages, Gerardo Perez, +and Lou Nassar for the development and release of this track.</p> + +<a name="121620"></a> +<h2>Dec. 16, 2020 New In-Silico PCR feature for assembly hubs</h2> +<p> +We are excited to announce assembly hubs can now perform In-Silico PCR. Assembly hub developers +have long been able to activate DNA and amino acid BLAT searches on their hubs by running gfServers +from their institution, and now with the new isPcr setting, they can enable In-Silico PCR searches too +using the same running gfServers. In-Silico PCR searches a sequence database with a pair of PCR primers, +using an indexing strategy for fast performance to find target regions across the genome. Browser users without an +institution to host gfServers can still benefit from this new feature by downloading and installing a virtual machine +<a href="help/gbib.html" target="_blank">Genome Browser in a Box (GBiB)</a>, and alternatively running gfServers on the + GBiB, all locally from a laptop. For more information see the <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs" +target="_blank">Assembly Hub Wiki</a> and the <a href="help/hubQuickStartAssembly.html" +target="_blank">Quick Start Guide to Assembly Hubs</a>.</p> + +<p> +We would like to thank Brian Raney and Gerardo Perez for their work on this release.</p> + +<a name="121520"></a> +<h2>Dec. 15, 2020 New V35 GENCODE genes track for Human (hg19/GRCh37)</h2> +<p> +We are pleased to announce a new GENCODE Genes annotation track, which corresponds +to <a href="http://www.ensembl.info/2020/08/20/ensembl-101-has-been-released/" +target="_blank">Ensembl 101</a>, for the: <a target="_blank" +href="../../cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgEncodeGencodeV35lift37">hg19/GRCh37</a> assembly. +The GENCODE V35 annotations were mapped to hg38/GRCh38 and then back-mapped +to the hg19/GRCh37 assembly. The gene set contains the following +tracks:</p> +<ul> + <li>Basic - a subset of the <em>Comprehensive set</em>.</li> + <li>Comprehensive - all GENCODE coding and non-coding transcript annotations, including + polymorphic pseudogenes. This includes both manual and automatic annotations.</li> + <li>Pseudogenes - all annotations except polymorphic pseudogenes.</li></ul> +<p> +Details on each release can be found on the <a target="_blank" +href="https://www.gencodegenes.org/">GENCODE site</a>. This includes <a target="_blank" +href="https://www.gencodegenes.org/human/stats.html">statistics on each release</a>. +<p>We would like to thank the <a target="_blank" +href="https://www.gencodegenes.org/pages/gencode.html">GENCODE project</a> for providing these +annotations. We would also like to thank Mark Diekhans and Lou Nassar for the development and +release of this track.</p> + +<a name="120920"></a> +<h2>Dec. 9, 2020 New Genome Browser: Hawaiian monk seal, neoSch1 (<em>Neomonachus schauinslandi</em>)</h2> +<p> +A genome browser is now available for the Hawaiian monk seal (<em>Neomonachus schauinslandi</em>) assembly +released in Jun. 2017 by the +<a href="https://www.hopkinsmedicine.org/profiles/results/directory/profile/5985613/alan-scott" +target="_blank">Johns Hopkins University</a> (ASM220157v1). +<h3>About the assembly:</h3> +<ul> + <li><b>UCSC Genome Browser assembly ID:</b> <a href="../../cgi-bin/hgGateway?db=neoSch1" + target="_blank">neoSch1</a></li> + <li><b>Sequencing/Assembly provider ID:</b> <a href="https://www.jhu.edu/"> +Johns Hopkins University</a></li> + <li><b>Assembly date:</b> Jun. 2017</li> + <li><B>Accession ID:</B> GCF_002201575.1</li> + <li><B>NCBI Genome ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/genome/8042" +TARGET="_blank">8042</A> (<em>Neomonachus schauinslandi</em>)</li> + <li><B>NCBI Assembly ID:</B> <A HREF="https://www.ncbi.nlm.nih.gov/assembly/GCF_002201575.1/" +TARGET="_blank">1137021</A></li> + <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/" +target="_blank" >FTP</a></li> + <li><a href="http://hgdownload.soe.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> <div class="container"> <div class="row"> <div class="col-sm-4"> <ul> <li>A. gambiae <a href="../cgi-bin/hgTrackUi?db=anoGam1&g=uniprot&position=default" target=_blank>(anoGam1)</a></li> <li>A. gambiae <a href="../cgi-bin/hgTrackUi?db=anoGam3&g=uniprot&position=default" target=_blank>(anoGam3)</a></li> <li>A. mellifera <a href="../cgi-bin/hgTrackUi?db=apiMel2&g=uniprot&position=default" @@ -548,31 +807,31 @@ target="_blank">Sun <em>et al</em></a>, and <a href="https://www.biorxiv.org/content/10.1101/2020.06.08.141127v1" target="_blank">Turakhia <em>et al</em></a> for making these data available. 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>. Will will continue to +<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" 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">