cf0611d6cdc0706ce0fb9f19f58a97bc951da578 dschmelt Mon Feb 1 12:41:57 2021 -0800 Announcement for COVID 6th data release refs #26836 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 9dacfa4..2bc8d36 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,68 @@ <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="012921"></a> +<h2>Jan. 29, 2021 January 29th SARS-CoV-2 Update</h2> +<p> +The UCSC Genome Browser is proud to share our sixth round of genetics data for the +SARS-CoV-2 virus (see our <a +href="#040320">first</a>, <a href="#050420">second</a>, <a href="#080720">third</a>, +and <a href="#102120">fourth</a> and <a href="010921">fifth</a> releases). +These data focus on the virus's mutations, evolution, and antibody +responses. As usual, these data are all open-access and interactive. For more information, +you can also visit out <a href="../covid19.html">COVID-19 home page</a>.</p> +<p> +Clicking on any of the track titles below will lead to the track description page, which includes additional information and allows for configuration of various display options. This release includes the following tracks:</p> +<ul> +<li><a href="/cgi-bin/hgTrackUi?db=wuhCor1&g=sarsCov2PhyloPub"> +Phylogeny: Public</a> - Updated 1/18/21 to contain more than 227k SARS-CoV-2 +genome sequences from <a +href="https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=SARS-CoV-2,%20taxid:2697049" +target="_blank">GenBank</a>, <a href="https://www.cogconsortium.uk/data/" +target="_blank">COG-UK</a>, the <a href="https://bigd.big.ac.cn/ncov/release_genome" +target="_blank">China National Center for Bioinformation</a>, and an inferred phylogenetic +tree. Since this track +is sourced from public databases, we offer +<a href="https://en.wikipedia.org/wiki/Variant_Call_Format">VCF</a> files with mutations for download.</li> +<li><a href="/cgi-bin/hgTrackUi?db=wuhCor1&g=spikeMuts">Spike protein mutations</a> - +Detailed annotations on spike protein mutations, based on community annotation from +mid-January 2021 at <a href="https://covariants.org/" target="_blank"> +CoVariants.org</a>, +supplemented by the Variants of SARS-CoV-2 page at Wikipeda. +Linked information includes date first sequenced, notes of clinical significance and +geographic incidence, and links to Nextstrain build, incidence charts and relevant publications. +Mutations in this track include: H69-, D80Y, S98F, A222V, N439K, Y453F, S477N, E484, +N501, D614G, A626S, P681H, A701B, V1122.</li> +<li><a href="/cgi-bin/hgTrackUi?db=wuhCor1&g=abEscape">Antibody escape mutation</a> - +Antibody binding scores from multiple +labs across all possible mutations of the Spike protein's receptor-binding domain (RBD).These data come +experiments using patient serum antibodies or monoclonal antibodies and a yeast-surface display system.</li> +</ul> + <a name="012621"></a> <h2>Jan. 26, 2021 New Genome Browser: Dog, canFam5 (<em>Canis lupus familiaris</em>)</h2> <p> A genome browser is now available for the <em>Canis lupus familiaris</em> assembly released in May 2019 by the <a href="https://umich.edu/" target="_blank"> University of Michigan</a> (UMICH_Zoey_3.1). <h3>About the assembly:</h3> <ul> <li><b>UCSC Genome Browser assembly ID:</b> <a href="../../cgi-bin/hgGateway?db=canFam5" target="_blank">canFam5</a></li> <li><b>Sequencing/Assembly provider ID:</b> <a href="https://umich.edu/"> University of Michigan</a></li> <li><b>Assembly date:</b> May 2019</li> <li><B>Accession ID:</B> GCA_005444595.1</li> <li><B>NCBI Genome ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/genome/85' TARGET='_blank'>85</A> (<em>Canis lupus familiaris</em>)</li>