cb69f436621e81c835b31bd83f83cd43433bda92 dschmelt Tue Oct 19 19:35:04 2021 -0700 Announcing VOC track #27926 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 06bd0f0..6bab644 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,55 @@ <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="102021"></a> +<h2>Oct. 20, 2021 SARS-CoV-2 Variants of Concern (VOC) track updated</h2> +<p>The UCSC Genom Browser is proud to share our latest update to the +SARS-CoV-2 browser, the updated +<a href="/cgi-bin/hgTrackUi?db=wuhCor1&g=variantMuts"> +Variants of Concern (VOC) track</a>. This data track +includes amino acid and nucleotide annotations for 10 different COVID variants, +including the Delta and Mu variants, mapped along the SARS-CoV-2 reference genome. +These variants are +<a href="https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/" + target="_blank">classified by the WHO</a> into several categories: Variants of Concern (VOC), +Variants of Interest (VOI), and Variants under Investigation (VUM). These tracks help +provide a more clear understanding of the mutations that comprise each named variant. +This track's items also include links to <a target="_blank" href="https://outbreak.info"> +Outbreak.info</a>, providing geographic distibutions for each variant. +</p> + +<p> +The underlying data is publically accessible and compatible with many analysis tools, including +our <a href="/cgi-bin/hgTables?db=wuhCor1">Table Browser</a>, + <a href="/cgi-bin/hgIntegrator">Data Integrator</a>, +and <a href="/goldenPath/help/api.html">JSON API</a>. More information on this track +can be found on the <a href="/cgi-bin/hgTrackUi?db=wuhCor1&g=variantMuts"> +Variants of Concern (VOC) track description page</a>.</p> + <a name="101221"></a> <h2>Oct. 18, 2021 Addition of GRCh38 patch 13 sequences to hg38</h2> <p> We are pleased to announce the addition of GRCh38 patch release 13 to the <a href="../../cgi-bin/hgGateway?db=hg38">hg38</a> assembly. hg38 has been updated with patches since its release in 2013. The GRC patch releases do not change any previously existing sequences; they simply add new sequences for fix patches or alternate haplotypes that correspond to specific regions of the main chromosome sequences. For most users, the patches are unlikely to make a difference and may complicate the analysis as they introduce more duplication.</p> <p> More information on how patch sequences are incorporated can be found on the <a href="http://genome.ucsc.edu/blog/patches/" target="_blank">Patching up the Genome</a> blog post. The blog post contains details about the new <a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/latest/" @@ -84,57 +109,30 @@ <li> The <b>p13/</b> subdirectory contains files for GRCh38.p13 (patch release 13). It has 640 sequences including alternate and fix sequences. </li> <li> The <b>latest/</b> symbolic link points to the subdirectory for the most recent patch version. </li> </ul> <p> We would like to thank the <a href="https://www.ncbi.nlm.nih.gov/grc" target="_blank">Genome Research Consortium</a> for creating the patches for hg38. We would also like to thank Galt Barber, Jairo Navarro, and Gerardo Perez at UCSC for implementing and testing the latest patch to the hg38 genome.</p> - -<a name="101521"></a> -<h2>Oct. 15, 2021</h2> -<p>The UCSC Genom Browser is proud to share our latest update to the -SARS-CoV-2 browser, the updated -<a href="/cgi-bin/hgTrackUi?db=wuhCor1&g=variantMuts"> -Variants of Concern (VOC) track</a>. This data track -includes amino acid and nucleotide annotations for 10 different COVID variants, -including the Delta and Mu variants, mapped along the SARS-CoV-2 reference genome. -These variants are -<a href="https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/" - target="_blank">classified by the WHO</a> into several categories: Variants of Concern (VOC), -Variants of Interest (VOI), and Variants under Investigation (VUM). These tracks help -provide a more clear understanding of the mutations that comprise each named variant. -This track's items also include links to <a target="_blank" href="https://outbreak.info"> -Outbreak.info</a>, providing geographic distibutions for each variant. -</p> -<p> - -The underlying data is publically accessible and compatible with many analysis tools, including -our <a href="/cgi-bin/hgTables?db=wuhCor1">Table Browser</a>, - <a href="/cgi-bin/hgIntegrator">Data Integrator</a>, -and <a href="/goldenPath/help/api.html">JSON API</a> tools. More information on this track -can be found on the <a href="/cgi-bin/hgTrackUi?db=wuhCor1&g=variantMuts"> -Variants of Concern (VOC) track description page</a>.</p> - - <a name="092721"></a> <h2>Sep. 27, 2021 JASPAR tracks for human (hg19/hg38)</h2> <p> We are pleased to announce the release of the <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=jaspar&position=default"> JASPAR Transcription Factors tracks</a> for human assemblies hg19/GRCh37 and hg38/GRCh38.</p> <p> These data represent genome-wide predicted binding sites for TF (transcription factor) binding profiles in the <a target="_blank" href="http://jaspar.genereg.net/about/"> JASPAR CORE collection</a>. This collection is an open-source database containing a curated, non-redundant set of binding profiles derived from published collections of experimentally defined transcription factor binding sites for eukaryotes.</a> <p> JASPAR has been a popular <a target="_blank" href="/cgi-bin/hgHubConnect">Public Hub</a> for many years and in collaboration with their group, the data can now be found as native