1ebfdf9a14d79221b7c27b932f7b0596c876755f gperez2 Wed Sep 15 16:36:00 2021 -0700 Updating news for cactus 241-way alignment track, refs #27519 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 6a21d3e..d6800ab 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,52 @@ <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="091321"></a> +<h2>Sep. 13, 2021 Cactus 241-way comparative genomics track for hg38</h2> +<p> +A new <a href="../../cgi-bin/hgTrackUi?db=hg38&g=cons241way&position=default"> 241-way +comparative genomics track</a> has been added to the human +(<a href="../../cgi-bin/hgGateway?db=hg38">GRCh38/hg38</a>) genome browser. This track +shows multiple alignments of 241 vertebrate species and measurements of evolutionary +conservation from the <a href="https://zoonomiaproject.org/the-project/" +target="_blank">Zoonomia Project</a>.</p> +<p> +The multiple alignments were generated using +the <a href="https://github.com/ComparativeGenomicsToolkit/cactus" +target="_blank">Cactus comparative genomics alignment system</a> and the base-wise +conservation scores were computed using phyloP from the PHAST package. For genome +assemblies not available in the genome browser, there are alternative assembly hub +genome browsers. Missing sequence in any assembly is highlighted in the track display +by regions of yellow when zoomed out and by Ns when displayed at base level.</p> +<p> +We would like to thank the Zoonomia Project for providing the data. We would also like to thank Hiram +Clawson, Brian Joseph Raney, Mark Diekhans, Lou Nassar, and Gerardo Perez for their efforts in +creating this track.</p> + <a name="083121"></a> <h2>Aug. 31, 2021 GENCODE Genes VM27 for mouse (mm39)</h2> <p> We are pleased to announce the release of the <a href="../../cgi-bin/hgTrackUi?db=mm39&c=chr12&g=knownGene">GENCODE Genes VM27</a> track for the mouse (<a href="../../cgi-bin/hgGateway?db=mm39">GRCm39/mm39</a>) Genome Browser.</p> <p> The GENCODE Genes track (version M27, Dec 2020) shows high-quality manual annotations merged with evidence-based automated annotations across the entire human genome generated by the <a href="https://www.gencodegenes.org/" target="_blank">GENCODE project</a>. By default, this track displays only the basic GENCODE set, splice variants, and non-coding genes. This track contains annotations on the reference chromosomes as well as assembly patches and alternative loci (haplotypes). </p> <p>