45aff60448645331b37278bb57faa67a2e0a7825 lrnassar Thu Jul 9 14:03:01 2020 -0700 Adding new assembly panPan3 to newsArch page #25720 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 69898c9..47896bb 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,97 @@ <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> <!-- ============= 2020 archived news ============= --> <a name="2020"></a> +<a name="071020"></a> +<h2>Jul. 10, 2020 New Genome Browsers: Dog (canFam4) and Bonobo (panPan3)</h2> +<p> +Genome browsers are now available for the <em>Canis lupus familiaris</em> assembly released +in March 2020 by <a href="https://www.uu.se/en" target="_blank">Uppsala University</a> +(UU_Cfam_GSD_1.0), and the <em>Pan paniscus</em> assembly released in May 2020 by the +<a href="https://www.washington.edu/" target="_blank">University of Washington</a> +(Mhudiblu_PPA_v0).</p> +<h3>About the assembly (canFam4):</h3> +<ul> + <li><b>UCSC Genome Browser assembly ID:</b> <a href="../../cgi-bin/hgGateway?db=canFam4" + target="_blank">canFam4</a></li> + <li><b>Sequencing/Assembly provider ID:</b> <a href="https://www.uu.se/en"> +Uppsala University</a></li> + <li><b>Assembly date:</b> Mar. 2020</li> + <li><B>Accession ID:</B> GCA_011100685.1</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> + <li><B>NCBI Assembly ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/assembly/6119491' +TARGET='_blank'>6119491</A></li> + <li><B>NCBI BioProject ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/bioproject/587469' +TARGET='_blank'>587469</A></li> + <li><B>NCBI BioSample ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/biosample/SAMN13230619' +TARGET='_blank'>SAMN13230619</A></li> + <li><b>Scaffold count: </b>2,198</li> + <li><b>Total size: </b>2,482,000,080</li> + <li><a href="../goldenPath/credits.html#dog_credits" +target="_blank" >Acknowledgments</a></li> +</ul> +<h3>About the assembly (panPan3):</h3> +<ul> + <li><b>UCSC Genome Browser assembly ID:</b> <a href="../../cgi-bin/hgGateway?db=panPan3" + target="_blank">panPan3</a></li> + <li><b>Sequencing/Assembly provider ID:</b> <a href="https://www.washington.edu/"> +University of Washington</a></li> + <li><b>Assembly date:</b> May 2020</li> + <li><B>Accession ID:</B> GCF_013052645.1</li> + <li><B>NCBI Genome ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/genome/10729' +TARGET='_blank'>10729</A> (<em>Pan paniscus</em>)</li> + <li><B>NCBI Assembly ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/assembly/7133581' +TARGET='_blank'>7133581</A></li> + <li><B>NCBI BioProject ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/bioproject/526933' +TARGET='_blank'>526933</A></li> + <li><B>NCBI BioSample ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/biosample/SAMN11123633' +TARGET='_blank'>SAMN11123633</A></li> + <li><b>Scaffold count: </b>4,357</li> + <li><b>Total size: </b>3,051,901,337</li> + <li><a href="../goldenPath/credits.html#bonobo_credits" +target="_blank" >Acknowledgments</a></li> +</ul> +<h3>Data and Downloads:</h3> +<ul> + <li><a href="../goldenPath/credits.html#dog_use" +target="_blank" >Data use conditions and restrictions</a></li> + <li><a href="../goldenPath/help/ftp.html" +target="_blank" >Rsync</a></li> + <li>FTP: <a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/canFam4/" +target="_blank" >Dog</a> and +<a href="ftp://hgdownload.soe.ucsc.edu/goldenPath/panPan3/" +target="_blank" >Bonobo</a></li> + <li>Downloads page: <a href="http://hgdownload.soe.ucsc.edu/downloads.html#dog" +target="_blank" >Dog</a> and +<a href="http://hgdownload.soe.ucsc.edu/downloads.html#bonobo" +target="_blank" >Bonobo</li> +</ul> +</p> + <a name="070720"></a> <h2>Jul. 07 2020 Three new SARS-CoV-2 (COVID) variation and comparative Genomics tracks published; 20th Anniversary of the Genome Browser</h2> <h3>New SARS-CoV-2 (COVID) Tracks</h3> <p> We are pleased to announce three new SARS-CoV-2 (COVID) data track about coronavirus variation and conservation. Like nearly all of our tracks, the data are open-access and downloadable through our <a href="http://hgdownload.soe.ucsc.edu/downloads.html#SARS-CoV-2"> Downloads page</a> or <a href="../../cgi-bin/hgTables">Table Browser</a> page. </p> <ul> <li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=PhyloCSF_smooth">PhyloCSF (Codon Substitution Frequency)</a> shows protein-coding potential score for each nucleotide in the genome in each of coding frame based on an aligning the SARS-CoV-2 genome with 44 Sarbecovirus genomes.</li> <li><a href="../../cgi-bin/hgTrackUi?db=wuhCor1&g=microdel">Microdeletions</a> shows sequence deletions found among thousands of SARS-CoV-2 genomes deposited in the