2fd50ddc65d39ab4d7e7b4860f2840d66ea014e4 dschmelt Thu Jun 24 14:27:08 2021 -0700 Releasing REVEL regfs #27141 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 5ee5fcc..4e05071 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,56 @@ <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="062421"></a> +<h2>June 24, 2021 New REVEL missense scores track for hg38 and hg19</h2> +<p> +The UCSC Genome Browser has just added the REVEL tracks to hg38 and hg19, +a much requested clinical dataset, now visualized and interactive with our tools. +REVEL scores predict the pathogenicity of missense variants for every possible +basepair change across the entire genome. This dataset bases its scores on 13 individual tools +to produce high predictive performance of common and rare mutations. To learn more about the +REVEL dataset, please visit their site below:</p> +<ul> + <li><a href="https://sites.google.com/site/revelgenomics/" target="_blank"> + https://sites.google.com/site/revelgenomics</a></li> +</ul> +<p> +To access these tracks on the Genome Browser, please visit their description pages below +and change the tracks' visibility.</p> +<ul> + <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=revel">REVEL track on hg38</a></li> + <li><a href="/cgi-bin/hgTrackUi?db=hg19&g=revel">REVEL track on hg19</a></li> +</ul> +</p> +<p> +Thanks to REVEL for providing these annotations, as well as +Max Haeussler and Dan Schmelter of the UCSC Genome Browser group for their +work in creating and releasing these tracks.</p> + <a name="061421"></a> <h2>Jun. 14, 2021 Updated Ensembl gene tracks for 48 assemblies (v104)</h2> <p> We are pleased to announce updated <a href="http://uswest.ensembl.org/info/genome/genebuild/index.html" target="_blank"> Ensembl gene annotation</a> tracks corresponding to <strong>v104</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&position=default" target=_blank>(dasNov3)</a></li> <li>Baboon <a href="../cgi-bin/hgTrackUi?db=papAnu4&g=ensGene&position=default" target=_blank>(papAnu4)</a></li> @@ -167,72 +193,72 @@ target=_blank>(xenTro9)</a></li> </ul></div> </div></div> <p> Thanks to Ensembl for providing these annotations, as well as Hiram Clawson and Lou Nassar of the UCSC Genome Browser group for their work in creating and releasing these tracks.</p> <a name="061021"></a> <h2>Jun. 10, 2021 Updated data for NCBI RefSeq tracks for human assembly hg19</h2> <p> We are pleased to announce the updated <a href="https://www.ncbi.nlm.nih.gov/genome/annotation_euk/ Homo_sapiens/109.20190905/#:~:text=NCBI%20Homo%20sapiens%20Updated%20Annotation%20Release% 20105.20201022&text=Updated%20Annotation%20Release%20105.20201022%20is,to%20update%20the%20annotated%20features" target="_blank">NCBI RefSeq Annotation Release 105.20201022</a> tracks for the -<a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=refSeqComposite&position=default">hg19/GRCh37</a> +<a href="/cgi-bin/hgTrackUi?db=hg19&g=refSeqComposite&position=default">hg19/GRCh37</a> assembly. 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><b>RefSeq All</b> – all annotations from the curated and predicted sets <li><b>RefSeq Curated</b> – curated annotations beginning with NM, NR, or NP <li><b>RefSeq Other</b> – all other RefSeq annotations not included in RefSeq All <li><b>RefSeq Alignments</b> – alignments of transcripts to the genome provided by RefSeq <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>Jun. 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.soe.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= http://genome.ucsc.edu/FAQ/FAQblat.html>BLAT</a> +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=https://genome.ucsc.edu/goldenPath/help/customTrack.html>custom track</a> -or creating a <a href=https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html>track hub</a>.</p> +<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/> 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> <p> GenArk assemblies can be found by searching the common name (e.g. - <a href="https://genome.ucsc.edu/h/GCF_001984765.1">American Beaver</a>) or GCA/GCF accession -(e.g. <a href="https://genome.ucsc.edu/h/GCF_001984765.1">GCF_001984765.1</a>) directly on the -<a href="http://genome.ucsc.edu/cgi-bin/hgGateway">Genome Browser Gateway page</a>. + <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 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.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.soe.ucsc.edu/hubs/birds/index.html">Birds</a></td> @@ -271,31 +297,31 @@ <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> <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="https://genome.ucsc.edu/cgi-bin/hgBlat?command=start">BLAT tool</a> to accommodate these assembly hubs and we call it Dynamic BLAT. Dynamic BLAT +<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> <p> We would like to thank NCBI RefSeq and Vertebrate Genome Project (VGP) for making these assemblies available. We would also like to thank Hiram Clawson, Mark Diekhans, Galt Barber, Lou Nassar, and Gerardo Perez, and the rest of the Browser team for their work on building the assembly hubs, creating GenArk, and extending BLAT to include these new assembly hubs.</p> <a name="051121"></a> <h2>May. 11, 2021 Vaccines track available for the SARS-CoV-2 Genome Browser</h2> <p> We are happy to announce the release of the <a href="../cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=vaccines">Vaccines</a> track for the UCSC