402499d2b0c1740a020abe56fd818e36da17df20 jnavarr5 Mon Aug 12 16:00:31 2024 -0700 Announcing the SpliceAI tracks for hg38 and hg19, refs #27141 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 8c35421..0cfea7a 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -54,30 +54,57 @@ <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 found <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 our <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>GitHub page</a>. Lastly, see our <a href="credits.html" target="_blank"> credits page</a> for acknowledgments of the data we host.</p> <!-- ============= 2024 archived news ============= --> <a name="2024"></a> +<a name="081224"></a> +<h2>Aug. 12, 2024 Illumina SpliceAI tracks for human (hg38 and hg19)</h2> +<p> +We pleased to announce the release of the <b>Illumina SpliceAI</b> tracks for the +<a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=spliceAI" target="_blank">hg38</a> and +<a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=spliceAI" target="_blank">hg19</a> +human assemblies. SpliceAI is an +<a href="https://github.com/Illumina/SpliceAI" target="_blank">open-source</a> deep +learning splicing prediction algorithm that can predict splicing alterations caused by DNA +variations. Such variants may activate nearby cryptic splice sites, leading to abnormal transcript +isoforms. SpliceAI was developed at Illumina; a <a href="https://spliceailookup.broadinstitute.org" +target="_blank">lookup tool</a> is provided by the Broad institute.</p> +<p> +<b>Important</b>: The SpliceAI data on the UCSC Genome Browser is directly from +Illumina. However, since SpliceAI refers to the algorithm, and not the +computed dataset, the data on the Broad server or other sources may have some differences between +them. The SpliceAI scores are made available by Illumina only for academic or not-for-profit +research only. By accessing the SpliceAI data, you acknowledge and agree that you may only use this +data for your own personal academic or not-for-profit research only, and not for any other purposes. +You may not use this data for any for-profit, clinical, or other commercial purpose without +obtaining a commercial license from Illumina, Inc. +</p> +<p> +We would like to thank Illumina for making this data available on the UCSC Genome Browser. We would +also like to thank Luis Nassar and Jairo Navarro for the creation and release of the tracks. +</p> + <a name="073124"></a> <h2>Jul. 31, 2024 GENCODE "KnownGene" v45lift37 release for human (hg19)</h2> <p> We are excited to announce the release of the <a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=knownGene" target="_blank">GENCODE "KnownGene" v45lift37</a> gene track for hg19. With this release, the previous 2013 UCSC Genes track will be frozen and made available in the <a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=knownGeneArchive" target="_blank">GENCODE/UCSC Genes Archive</a> superTrack for reproducibility. As new GENCODE tracks are made available, previous versions will also be available in the archive. Beginning with this update, the "KnownGene" track will use GENCODE v45 gene models lifted to hg19, which replaces the old UCSC transcript IDs with the official GENCODE IDs. </p> <p> The following is an example of some GENCODE IDs that will replace the UCSC IDs in the update: