8d9c032cec6621134038a076a40d8a687ea62cff kuhn Tue Jun 29 11:20:39 2021 -0700 tiny tweaks for consistency diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 1764a1e..7c8fe81 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -91,31 +91,31 @@ </ul> <p> To access these tracks on the Genome Browser, please visit their description pages below and change the tracks' visibility.</p> <ul> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=revel">REVEL track on hg38</a></li> <li><a href="/cgi-bin/hgTrackUi?db=hg19&g=revel">REVEL track on hg19</a></li> </ul> </p> <p> Thanks to REVEL for providing these annotations, as well as Max Haeussler and Dan Schmelter of the UCSC Genome Browser group for their work in creating and releasing these tracks.</p> <a name="061421"></a> -<h2>Jun. 14, 2021 Updated Ensembl gene tracks for 48 assemblies (v104)</h2> +<h2>June 14, 2021 Updated Ensembl gene tracks for 48 assemblies (v104)</h2> <p> We are pleased to announce updated <a href="http://uswest.ensembl.org/info/genome/genebuild/index.html" target="_blank"> Ensembl gene annotation</a> tracks corresponding to <strong>v104</strong> for the following assemblies:</p><br> <div class="container"> <div class="row"> <div class="col-sm-4"> <ul> <li>Armadillo <a href="../cgi-bin/hgTrackUi?db=dasNov3&g=ensGene&position=default" target=_blank>(dasNov3)</a></li> <li>Baboon <a href="../cgi-bin/hgTrackUi?db=papAnu4&g=ensGene&position=default" target=_blank>(papAnu4)</a></li> <li>Bison <a href="../cgi-bin/hgTrackUi?db=bisBis1&g=ensGene&position=default" target=_blank>(bisBis1)</a></li> @@ -211,55 +211,55 @@ target=_blank>(tarSyr2)</a></li> <li>Tetraodon <a href="../cgi-bin/hgTrackUi?db=tetNig2&g=ensGene&position=default" target=_blank>(tetNig2)</a></li> <li>Turkey <a href="../cgi-bin/hgTrackUi?db=melGal5&g=ensGene&position=default" target=_blank>(melGal5)</a></li> <li>X. tropicalis <a href="../cgi-bin/hgTrackUi?db=xenTro9&g=ensGene&position=default" target=_blank>(xenTro9)</a></li> </ul></div> </div></div> <p> Thanks to Ensembl for providing these annotations, as well as Hiram Clawson and Lou Nassar of the UCSC Genome Browser group for their work in creating and releasing these tracks.</p> <a name="061021"></a> -<h2>Jun. 10, 2021 Updated data for NCBI RefSeq tracks for human assembly hg19</h2> +<h2>June 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="/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> +<h2>June 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="/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="help/customTrack.html">custom track</a> or creating a <a href="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>, @@ -333,31 +333,31 @@ <p> As mentioned above, assembly hubs in the GenArk allow for sequence alignment using the BLAT tool. We extended our traditional <a href="../cgi-bin/hgBlat?command=start">BLAT tool</a> to accommodate these assembly hubs and we call it Dynamic BLAT. 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> +<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> <li> The Moderna mRNA-1273 sequence as sequenced by the @@ -367,31 +367,31 @@ <p> The protein encoded by the three sequences has two amino acid substitutions compared to the SARS-CoV-2 S glycoprotein. These vaccines include two variations compared to the reference Spike sequence to stabilize the shape into a pre-infection structure that delivers a better immune response, S:K986P and S:V987P. See also: <a href="https://cen.acs.org/pharmaceuticals/vaccines/tiny-tweak-behind-COVID-19/98/i38" target="_blank">The tiny tweak behind COVID-19 vaccines</a>. More information about this track can be found on the <a href="../cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=vaccines">description page</a>. <p> We want to thank the <a href="https://twitter.com/Fire__Lab" target="_blank">Andrew Fire lab</a>, Stanford University School of Medicine for providing the sequencing data of these vaccines. We also want to thank Hiram Clawson and Jairo Navarro for the creation and release of this track.</p> <a name="050421"></a> -<h2>May. 04, 2021 New Genome Browser: Rat, rn7 (<em>Rattus norvegicus</em>)</h2> +<h2>May 04, 2021 New Genome Browser: Rat, rn7 (<em>Rattus norvegicus</em>)</h2> <p> A genome browser is now available for the <em>Rattus norvegicus</em> assembly released in Nov. 2020 by the <a href="https://www.darwintreeoflife.org/" target="_blank"> Darwin Tree of Life Project</a> at the <a href="https://www.sanger.ac.uk/" target="_blank"> Wellcome Sanger Institute</a> (mRatBN7.2). <h3>About the assembly:</h3> <ul> <li><b>UCSC Genome Browser assembly ID:</b> <a href="../../cgi-bin/hgGateway?db=rn7" target="_blank">rn7</a></li> <li><b>Sequencing/Assembly provider ID:</b> <a href="https://www.sanger.ac.uk/" target="_blank">Wellcome Sanger Institute</a></li> <li><b>Assembly date:</b> Nov. 2020</li> <li><B>Accession ID:</B> GCF_015227675.2</li> <li><B>NCBI Genome ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/genome/73' TARGET='_blank'>73</A> (<em>Rattus norvegicus</em>)</li> <li><B>NCBI Assembly ID:</B> <A HREF='https://www.ncbi.nlm.nih.gov/assembly/9079111'