0017a306a24829adbd860a5deb7e9d4ece131df9 gperez2 Tue Jun 1 09:56:54 2021 -0700 Updating news for GenArk and Dynamic BLAT, refs #27556 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 863f305..9d6c262 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -39,30 +39,130 @@ </div> <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="060121"></a> +<h2>Jun. 1, 2021 Genome Archive (GenArk) hubs and Dynamic BLAT</h2> +<p> +Do you have a favorite species or a research organism for which you'd like to visualize +the genomic sequence? With the recent addition of genomic assemblies for more than 1,300 +species, it's possible that your favorite is now available in the UCSC Genome Browser. +Check <a href=https://hgdownload.soe.ucsc.edu/hubs/>this list</a> of new assemblies +to see if yours is a click away. Each of these Genome Browser assembly hubs comes pre-loaded +with several annotation tracks, gene models, and the ability to align genomic sequence to +the reference assembly using the <a href= http://genome.ucsc.edu/FAQ/FAQblat.html>BLAT</a> +alignment tool. You can add your own data to your view of the assembly hub by uploading a +<a href=https://genome.ucsc.edu/goldenPath/help/customTrack.html>custom track</a> +or creating a <a href=https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html>track hub</a>.</p> +<p> +We call this group of assembly hubs, the <a href=https://hgdownload.soe.ucsc.edu/hubs/> +Genome Archive (GenArk)</a>. The genomes in the GenArk are sourced from +<a href=https://www.ncbi.nlm.nih.gov/refseq/ target="_blank">NCBI RefSeq</a>, +the <a href="https://vertebrategenomesproject.org/" target="_blank">Vertebrate Genomes Project (VGP)</a> +and other projects. See the complete list of assembly hubs <a target="_blank" +href="https://hgdownload.soe.ucsc.edu/hubs/UCSC_GI.assemblyHubList.txt">here</a>.</p> +<p> +GenArk assemblies can be found by searching the common name (e.g. + <a href="https://genome.ucsc.edu/h/GCF_001984765.1">American Beaver</a>) or GCA/GCF accession +(e.g. <a href="https://genome.ucsc.edu/h/GCF_001984765.1">GCF_001984765.1</a>) directly on the +<a href="http://genome.ucsc.edu/cgi-bin/hgGateway">Genome Browser Gateway page</a>. +A full list can also be seen on the <a +href="https://hgdownload.soe.ucsc.edu/hubs">GenArk portal</a> which +is organized by phylogenetic groups and projects:<br> + +<div align="left"> +<table class="stdTbl"> + <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/primates/index.html">Primates</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/primates/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/primates/trackData.html">Track statistics</a></td></tr> + + <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/mammals/index.html">Mammals</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/mammals/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/mammals/trackData.html">Track statistics</a></td></tr> + + <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/birds/index.html">Birds</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/birds/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/birds/trackData.html">Track statistics</a></td></tr> + + <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/fish/index.html">Fishes</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/fish/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/fish/trackData.html">Track statistics</a></td></tr> + + <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/vertebrate/index.html">Vertebrates</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/vertebrate/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/vertebrate/trackData.html">Track statistics</a></td></tr> + + <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/invertebrate/index.html">Invertebrates</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/invertebrate/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/invertebrate/trackData.html">Track statistics</a></td></tr> + + <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/fungi/index.html">Fungi</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/fungi/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/fungi/trackData.html">Track statistics</a></td></tr> + + <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/plants/index.html">Plants</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/plants/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/plants/trackData.html">Track statistics</a></td></tr> + + <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/VGP/index.html">VGP</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/VGP/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/VGP/trackData.html">Track statistics</a></td></tr> + + <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/legacy/index.html">Legacy</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/legacy/asmStats.html">Assembly statistics</a></td> + <td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/legacy/trackData.html">Track statistics</a></td></tr> + + <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/globalReference/index.html">Global Reference</a></td> + <td><a></a></td> + <td><a></a></td></tr> + + <tr><td><a target="_blank" href="https://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hubIndex.html">Mouse Strains</a></td> + <td><a></a></td> + <td><a></a></td></tr> + +</table></div></p> +<p> +The number of NCBI RefSeq assemblies has been increasing each year, and we expect the trend to continue as assemblies +from VGP, and other projects are released. Our next step is to add additional clades to GenArk including archaea, +viruses, and bacteria.</p> + +<p> +As mentioned above, assembly hubs in the GenArk allow for sequence alignment using the BLAT tool. We extended our traditional +<a href="https://genome.ucsc.edu/cgi-bin/hgBlat?command=start">BLAT tool</a> to accommodate these assembly hubs and we call it +<a target="_blank" href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs#Adding_BLAT_servers">Dynamic BLAT</a>. Dynamic BLAT +pre-computes index genomes files, which allows assemblies to have a BLAT server without needing it to be resident in the +computer's memory. Dynamic BLAT allows us to offer BLAT services on nearly all of our GenArk assemblies, with a few exceptions +due to excessive genome size.</p> + +<p> +We would like to thank NCBI RefSeq and Vertebrate Genome Project (VGP) for making these assemblies available. We would also +like to thank Hiram Clawson, Mark Diekhans, Galt Barber, Lou Nassar, and Gerardo Perez, and the rest of the Browser team +for their work on building the assembly hubs, creating GenArk, and extending BLAT to include these new assembly hubs.</p> + + <a name="051121"></a> <h2>May. 11, 2021 Vaccines track available for the SARS-CoV-2 Genome Browser</h2> <p> We are happy to announce the release of the <a href="../cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=vaccines">Vaccines</a> track for the UCSC SARS-CoV-2 Genome Browser. This track shows the alignment of three different mRNA vaccine sequences to the coronavirus genome: </p> <ol> <li> The BioNTech/Pfizer BNT-162b2 sequence as published by the World Health Organization (WHO)</li> <li> The reconstructed BioNTech/Pfizer BNT-162b2 RNA as sequenced by the <a href="https://firelab.sites.stanford.edu/" target="_blank">Andrew Fire lab</a>, Stanford University School of Medicine</li>