801f36c6c9fe7974ce8c89427dd7417697c28ef5 lrnassar Fri May 1 16:11:51 2020 -0700 News release for 2nd coronavirus data release refs #25343 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 8507b5e..bc33767 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,32 +40,139 @@ <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> <!-- ============= 2020 archived news ============= --> <a name="2020"></a> +<a name="050420"></a> +<h2>May 4, 2020 May 4th data release for SARS-CoV-2 genome browser</h2> +<p> +We are pleased to announce our second data release for the <a target="_blank" +href="/cgi-bin/hgTracks?db=wuhCor1">coronavirus genome browser</a>. Much like our +<a href="#040320">first release</a>, this includes a variety of annotation types such as CRISPR +tracks, protein structure and interaction tracks, immunology tracks, and a 119-way multiple +sequence alignment.</p> +<p> +One new track we would like to highlight is the <a target="_blank" +href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=publicAnnots">Crowd-Sourced Data</a> track. +This track displays annotations made via a public spreadsheet available at +<a target="_blank" href="http://bit.ly/cov2annots">http://bit.ly/cov2annots</a>. Any user +can freely contribute to the spreadsheet, after which the annotations will display in +the public coronavirus genome browser.</a> +<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. <br><br>This release includes the following tracks:</p><br> + +<ul> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=publicAnnots"> +Crowd-Sourced Data</a> - This track shows varied annotations submitted by users via a +public spreadsheet available at <a target="_blank" href="http://bit.ly/cov2annots"> +http://bit.ly/cov2annots</a>.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=cas13Crispr"> +Cas13 CRISPR</a> - This track shows the in silico design of crRNAs for Cas13 using +the tool <a target="_blank" href="https://github.com/QilabGitHub/nCov2019_Guide_Design"> +nCov2019_Guide_Design</a>, as described in Abbott et al, 2020.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=crisprDet"> +CRISPR Detection Guides</a> - This track shows the locations of CRISPR detection +guides and flanking primers, containing data aggregated from three institutions.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=artic"> +ARTIC Primers</a> - This track shows the primers for the <a target="_blank" +href="https://artic.network/">ARTIC network</a> SARS-CoV-2 sequencing protocol, Version 3.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=gordon2"> +Human Interacting Proteins</a> - This track shows human protein-protein interactions +as described by <a target="_blank" +href="https://www.biorxiv.org/content/10.1101/2020.03.22.002386v1.full.pdf+html">Gordon et al, 2020</a>.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=pdb"> +Protein Data Bank (PDB) Structures</a> - This track shows alignments of sequences +with known protein structures in the <a target="_blank" href="https://www.rcsb.org/"> +Protein Data Bank.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=rnaStructRangan"> +Rangan et al. RNA predictions</a> - This track shows the locations of RNA structure +predictions reported in <a target="_blank" href="https://doi.org/10.1101/2020.03.27.012906"> +Rangan et al, 2020</a>.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=rfam"> +Rfam</a> - This track shows coronavirus-specific structured RNA families from the +<a target="_blank" href="https://rfam.org/">Rfam database</a>.</li> +<li> +<a target="_blank" href="https://www.cell.com/pb-assets/products/coronavirus/CELL_CELL-D-20-00765.pdf"> +Kim et al, Cell 2020.</a> - Tracks created from this publication include: + <ul> + <li> + <a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=kimTranscripts"> + Kim Transcripts</a> - This track shows predicted and experimental representations of the + SARS-CoV-2 transcriptome based on long-read Nanopore sequencing.</li> + <li> + <a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=kimNp"> + Kim RNA Breakpoints</a> - This track shows the locations of RNA transcript breakpoints + as determined by Nanopore and DNA Nanoball MGISEQ sequencing.</li> + <li> + <a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=kimRnaMod"> + Kim RNA Modifications</a> - This track shows the locations of RNA-modifications as + determined by Nanopore sequencing.</li> + </ul></li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=poranHla1"> +Poran HLA</a> - This track shows putative epitopes for CD4+ and CD8+ T cells whose HLA +binding properties cover over 99% for US, European, and Asian populations, for both +HLA-I and HLA-II.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=targets"> +T-Reactive Epitopes</a> - This track shows T-cell reactive epitopes in patients and +donors as described by <a target="_blank" +href="https://www.medrxiv.org/content/10.1101/2020.04.17.20061440v1.full.pdf+html"> +Braun et al, 2020</a>.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=strainCons119way"> +119-Way Coronavirus Alignment</a> - This track shows multiple alignments of 119 coronavirus +sequences, aligned to the SARS-CoV-2 reference. It includes both 2019/2020 outbreak sequences +and more distantly related vertebrate host sequences.</li> +</ul> +<p> +We would like to thank the publication authors Abbott et al, Gordon et al, Rangan et al, +Poran et al, and Braun et al for making these data available. We would also like to thank +<a target="_blank" href="https://rfam.xfam.org/">Rfam</a>, <a target="_blank" +href="https://www.rcsb.org/">PDB</a>, <a target="_blank" href="https://mammoth.bio/"> +Mammoth Biosciences</a>, the <a target="_blank" href="https://www.sabetilab.org/"> +Sabeti Lab</a> at the Broad Institute, and the <a target="_blank" href="http://sanjanalab.org/"> +Sanjana Lab</a> at New York University.</p> +<p> +Lastly, we would like to thank Kord Kober and Kiley Charbonneau from the <a target="_blank" +href="https://kober.ucsf.edu/">Kober lab</a> at UCSF for their contributions to the +crowd-sourced data track, as well as David Haussler, Jason Fernandes, Manny Ares, Justin Sim, +Alinne Gonzalez Armenta, and the rest of the scientists at UCSC (and the Genome Browser) +for making these tracks possible.</p> + <a name="042920"></a> -<h2>Apr. 29, 2019 Updated NCBI RefSeq gene tracks for 43 assemblies</h2> +<h2>Apr. 29, 2020 Updated NCBI RefSeq gene tracks for 43 assemblies</h2> <p> We are pleased to announce a combination of both updated and new <a href="https://www.ncbi.nlm.nih.gov/refseq/" target="_blank"> NCBI RefSeq gene annotation</a> tracks for the following 43 assemblies:</p><br> <div class="container"> <div class="row"> <div class="col-sm-4"> <ul> <li>African clawed frog <a href="../cgi-bin/hgTrackUi?db=xenLae2&g=refSeqComposite" target=_blank>(xenLae2)</a></li> <li>Armadillo <a href="../cgi-bin/hgTrackUi?db=dasNov3&g=refSeqComposite" target=_blank>(dasNov3)</a></li> <li>Baboon <a href="../cgi-bin/hgTrackUi?db=papAnu4&g=refSeqComposite" target=_blank>(papAnu4)</a></li> @@ -271,31 +378,31 @@ As with all our videos, a transcript is provided for those who wish to review the content before watching. </p> <ul> <li> Part One: Getting around in the Browser</li> <li> Part Two: Configuring the Browser </li> <li> Part Three: Configuration + DNA Navigation </li> </ul> </p> <a name="041420"></a> -<h2>Apr. 14, 2019 Updated Ensembl gene tracks for 43 assemblies</h2> +<h2>Apr. 14, 2020 Updated Ensembl gene tracks for 43 assemblies</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>v99</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" target=_blank>(dasNov3)</a></li> <li>Bison <a href="../cgi-bin/hgTrackUi?db=bisBis1&g=ensGene" target=_blank>(bisBis1)</a></li> <li>Bonobo <a href="../cgi-bin/hgTrackUi?db=panPan2&g=ensGene" target=_blank>(panPan2)</a></li>