63656c54eadd4f059fd7ac184c57f53d2081db29 gperez2 Tue Feb 13 14:09:51 2024 -0800 Announcing the release of All GENCODE for hg38, hg19 (V45), and mm39 (VM34). refs #32411 #32413 #32412 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 5e1373c..9450ef1 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,30 +51,75 @@ </div> <p>You can sign-up to get these announcements via our <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a> email list. We send around one short announcement email every two weeks.</p> <p>Smaller software changes are not announced here. A summary of the three-weekly release changes can be <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. For the full list of our daily code changes head to <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>our GitHub page</a>.</p> <!-- ============= 2024 archived news ============= --> <a name="2024"></a> +<a name="021424"></a> +<h2>Feb. 14, 2024 New GENCODE gene tracks: Human V45 (hg19/hg38) - Mouse VM34 +(mm39)</h2> +<p> +We are happy to announce new GENCODE Gene annotation tracks, which correspond +to <a href="https://www.ensembl.info/2024/01/11/ensembl-111-has-been-released/" +target="_blank">Ensembl 111</a>, for three assemblies: <a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeGencodeV45lift37">hg19/GRCh37</a>, +<a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=wgEncodeGencodeV45">hg38/GRCh38</a>, +and +<a target="_blank" href="/cgi-bin/hgTrackUi?db=mm39&c=chr12&g=wgEncodeGencodeVM34">mm39/GRCm39</a>. +<a target="_blank" href="https://www.gencodegenes.org/">GENCODE</a> provides gene annotations with +high accuracy based on biological evidence and for the benefit of biomedical research and genome +interpretation. For human, the GENCODE V45 annotations were mapped to hg38/GRCh38 and then back-mapped +to the hg19/GRCh37 assembly. For all three assemblies, the 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 and mm39 assemblies also include the following track that is not available on hg19: +</p> +<ul> + <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> +<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 Gerardo Perez for the development and +release of these tracks.</p> + <a name="021224"></a> <h2>Feb. 12, 2024 Variants of Concern SARS-CoV-2 track updated with Omicron variants</h2> <p> We are happy to announce an update to the <a href="/cgi-bin/hgTrackUi?db=wuhCor1&position=default&g=variantMuts" target="_blank">Variants of Concern</a> track to include the latest WHO-designated variants of concern (VOC). The evolving SARS-CoV-2 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> In this update, the following Omicron variants were added to the Variants of Concern track:</p> <div class="container"> <div class="row"> <div class="col-sm-4">