54332d10a159802c8310bc7d33bd66c85058426d gperez2 Thu Jun 10 09:02:47 2021 -0700 Updating news for the ncbiRefSeq track update, refs #27575 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 1f74beb..e53131f 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,54 @@ <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="061021"></a> +<h2>Jun. 10, 2021 Updated data for NCBI RefSeq tracks for human assembly hg19</h2> +<p> +We are pleased to announce the updated <a href="https://www.ncbi.nlm.nih.gov/genome/annotation_euk/ +Homo_sapiens/109.20190905/#:~:text=NCBI%20Homo%20sapiens%20Updated%20Annotation%20Release% +20105.20201022&text=Updated%20Annotation%20Release%20105.20201022%20is,to%20update%20the%20annotated%20features" +target="_blank">NCBI RefSeq Annotation Release 105.20201022</a> tracks for the +<a href="http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=refSeqComposite&position=default">hg19/GRCh37</a> +assembly. For all of these tracks, the alignments and coordinates are provided by RefSeq. +These tracks are organized in a composite track that includes:</p> +<ul> + <li><b>RefSeq All</b> – all annotations from the curated and predicted sets + <li><b>RefSeq Curated</b> – curated annotations beginning with NM, NR, or NP + <li><b>RefSeq Other</b> – all other RefSeq annotations not included in RefSeq All + <li><b>RefSeq Alignments</b> – alignments of transcripts to the genome provided by RefSeq + <li><b>RefSeq Diffs</b> – alignment differences between the human reference genome(s) and RefSeq transcripts + <li><b>RefSeq Select</b> – a single Select transcript representative for each protein-coding gene + <li><b>RefSeq HGMD</b> – transcripts with clinical variants in Human Gene Mutation Database +</ul> +<p> +We would like to thank NCBI and the RefSeq Annotation database for collecting and curating these data. +We would also like to thank Hiram Clawson, Lou Nassar, and Gerardo Perez for developing and releasing these tracks. +</p> + <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/>