73c100526aa0bad1111e65bc746734dc3b859796 gperez2 Mon Dec 22 14:45:20 2025 -0800 Releasing and announcing the EVA Release 8 tracks, refs #36512 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 9693d92eb40..bb957dad930 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,51 +52,200 @@ <p>You can sign-up to get these announcements via our <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a> email list. We send around one short announcement email every two weeks.</p> <p>Smaller software changes are not announced here. A summary of the three-weekly release changes can be found <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. For the full list of our daily code changes head to our <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>GitHub page</a>. Lastly, see our <a href="credits.html" target="_blank"> credits page</a> for acknowledgments of the data we host.</p> <!-- ============= 2025 archived news ============= --> <a name="2025"></a> +<a name="121925"></a> +<h2>Dec. 19, 2025 EVA SNP release 8 for 41 assemblies</h2> +<p> +We are pleased to announce the release of the EVA SNP Release 8 tracks for 41 assemblies. +These tracks contain mappings of single nucleotide variants and small insertions and deletions +(indels) — collectively Simple Nucleotide Variants (SNVs) — from the European Variation +Archive (<a href="https://www.ebi.ac.uk/eva/" target="_blank">EVA</a>) Release 8. The full list of +assemblies that contain the EVA SNP release 8 track is below:</p> + +<p> +<div class="container"> + <div class="row"> + <div class="col-sm-4"> + <ul> + <li>A. gambiae <a href="../cgi-bin/hgTrackUi?db=anoGam3&g=evaSnp8" + target="_blank">(anoGam3)</a></li> + <li>C. intestinalis <a href="../cgi-bin/hgTrackUi?db=ci3&g=evaSnp8" + target="_blank">(ci3)</a></li> + <li>Bison <a href="../cgi-bin/hgTrackUi?db=bisBis1&g=evaSnp8" + target="_blank">(bisBis1)</a></li> + <li>Cat <a href="../cgi-bin/hgTrackUi?db=felCat8&g=evaSnp8" + target="_blank">(felCat8)</a>, + <a href="../cgi-bin/hgTrackUi?db=felCat9&g=evaSnp8" + target="_blank">(felCat9)</a></li> + <li>Chicken <a href="../cgi-bin/hgTrackUi?db=galGal4&g=evaSnp8" + target="_blank">(galGal4)</a>, + <a href="../cgi-bin/hgTrackUi?db=galGal5&g=evaSnp8" + target="_blank">(galGal5)</a>, + <a href="../cgi-bin/hgTrackUi?db=galGal6&g=evaSnp8" + target="_blank">(galGal6)</a></li> + <li>Chimp <a href="../cgi-bin/hgTrackUi?db=panTro4&g=evaSnp8" + target="_blank">(panTro4)</a>, + <a href="../cgi-bin/hgTrackUi?db=panTro5&g=evaSnp8" + target="_blank">(panTro5)</a></li></li> + <li>Cow <a href="../cgi-bin/hgTrackUi?db=bosTau6&g=evaSnp8" + target="_blank">(bosTau6)</a>, + <a href="../cgi-bin/hgTrackUi?db=bosTau7&g=evaSnp8" + target="_blank">(bosTau7)</a>, + <a href="../cgi-bin/hgTrackUi?db=bosTau9&g=evaSnp8" + target="_blank">(bosTau9)</a></li> + <li>Crab-eating macaque <a href="../cgi-bin/hgTrackUi?db=macFas5&g=evaSnp8" + target="_blank">(macFas5)</a></li> + <li>D. melanogaster <a href="../cgi-bin/hgTrackUi?db=dm6&g=evaSnp8" + target="_blank">(dm6)</a></li> + </ul></div> + <div class="col-sm-4"> + <ul> + <li>Dog <a href="../cgi-bin/hgTrackUi?db=canFam3&g=evaSnp8" + target="_blank">(canFam3)</a></li> + <li>C. elegans <a href="../cgi-bin/hgTrackUi?db=ce11&g=evaSnp8" + target="_blank">(ce11)</a></li> + <li>Gorilla <a href="../cgi-bin/hgTrackUi?db=gorGor3&g=evaSnp8" + target="_blank">(gorGor3)</a>, + <a href="../cgi-bin/hgTrackUi?db=gorGor4&g=evaSnp8" + target="_blank">(gorGor4)</a></li> + <li>Green monkey <a href="../cgi-bin/hgTrackUi?db=chlSab2&g=evaSnp8" + target="_blank">(chlSab2)</a></li> + <li>Horse <a href="../cgi-bin/hgTrackUi?db=equCab3&g=evaSnp8" + target="_blank">(equCab3)</a></li> + <li>Marmoset <a href="../cgi-bin/hgTrackUi?db=calJac3&g=evaSnp8" + target="_blank">(calJac3)</a></li> + <li>Mouse <a href="../cgi-bin/hgTrackUi?db=mm10&g=evaSnp8" + target="_blank">(mm10)</a>, + <a href="../cgi-bin/hgTrackUi?db=mm39&g=evaSnp8" + target="_blank">(mm39)</a></li> + <li>Nile tilapia <a href="../cgi-bin/hgTrackUi?db=oreNil2&g=evaSnp8" + target="_blank">(oreNil2)</a></li> + <li>Orangutan <a href="../cgi-bin/hgTrackUi?db=ponAbe3&g=evaSnp8" + target="_blank">(ponAbe3)</a></li> + </ul></div> + <div class="col-sm-4"> + <ul> + <li>Pig <a href="../cgi-bin/hgTrackUi?db=susScr3&g=evaSnp8" + target="_blank">(susScr3)</a>, + <a href="../cgi-bin/hgTrackUi?db=susScr11&g=evaSnp8" + target="_blank">(susScr11)</a></li> + <li>Rat <a href="../cgi-bin/hgTrackUi?db=rn5&g=evaSnp8" + target="_blank">(rn5)</a>, + <a href="../cgi-bin/hgTrackUi?db=rn6&g=evaSnp8" + target="_blank">(rn6)</a>, + <a href="../cgi-bin/hgTrackUi?db=rn7&g=evaSnp8" + target="_blank">(rn7)</a></li> + <li>Rhesus <a href="../cgi-bin/hgTrackUi?db=rheMac8&g=evaSnp8" + target="_blank">(rheMac8)</a>, + <a href="../cgi-bin/hgTrackUi?db=rheMac10&g=evaSnp8" + target="_blank">(rheMac10)</a></li> + <li>S. cerevisiae <a href="../cgi-bin/hgTrackUi?db=sacCer3&g=evaSnp8" + target="_blank">(sacCer3)</a></li> + <li>Sheep <a href="../cgi-bin/hgTrackUi?db=oviAri3&g=evaSnp8" + target="_blank">(oviAri3)</a>, + <a href="../cgi-bin/hgTrackUi?db=oviAri4&g=evaSnp8" + target="_blank">(oviAri4)</a></li> + <li>Turkey <a href="../cgi-bin/hgTrackUi?db=melGal5&g=evaSnp8" + target="_blank">(melGal5)</a></li> + <li>Zebra finch <a href="../cgi-bin/hgTrackUi?db=taeGut2&g=evaSnp8" + target="_blank">(taeGut2)</a></li> + <li>Zebrafish <a href="../cgi-bin/hgTrackUi?db=danRer7&g=evaSnp8" + target="_blank">(danRer7)</a>, + <a href="../cgi-bin/hgTrackUi?db=danRer10&g=evaSnp8" + target="_blank">(danRer10)</a>, + <a href="../cgi-bin/hgTrackUi?db=danRer11&g=evaSnp8" + target="_blank">(danRer11)</a></li> + </ul></div> + </div> +</div></p> + +<p> +These variants are classified by EVA into one of the following <a target="_blank" +href="http://www.sequenceontology.org/">sequence ontology</a> terms: +</p> +<ul> + <li> <b>substitution</b> — + A single nucleotide in the reference is replaced by another, alternate allele. + <li> <b>deletion</b> — + One or more nucleotides are deleted. The representation in the database is to + display one additional nucleotide in both the Reference field (Ref) and the + Alternate Allele field (Alt). E.g., a variant that is a deletion of an A + may be represented as Ref = GA and Alt = G. + <li> <b>insertion</b> — + One or more nucleotides are inserted. The representation in the database is to + display one additional nucleotide in both the Reference field (Ref) and the + Alternate Allele field (Alt). E.g., a variant that is an insertion of a T may + be represented as Ref = G and Alt = GT. + <li> <b>delins</b> — + Similar to a tandem repeat, in that the runs of Ref and Alt Alleles are of + different length, except that there is more than one type of nucleotide, + e.g., Ref = CCAAAAACAAAAACA, Alt = ACAAAAAC. + <li> <b>multipleNucleotideVariant</b> — + More than one nucleotide is substituted by an equal number of different + nucleotides, e.g., Ref = AA, Alt = GC. + <li> <b>sequence alteration</b> — + A parent term meant to signify a deviation from another sequence. Can be + assigned to variants that have not been characterized yet. +</ul> +<p> +The variants have also been annotated with our <a href="/cgi-bin/hgVai" target="_blank">Variant +Annotation Integrator</a> tool with functional classes such as synonymous variant, +missense variant, stop gained, etc. For additional details on the track colors, +as well as the filters and metadata on each variant, see the +<a href="/cgi-bin/hgTrackUi?db=anoGam3&c=chr2R&g=evaSnpContainer&position=default#TRACK_HTML" + target="_blank">track description page</a>.</p> + +<p> +We would like to thank the <a href="https://www.ebi.ac.uk/eva/" target="_blank">European Variation +Archive</a> for making these data publicly available. We would also like to thank Gerardo Perez, Luis Nassar, +and Angie Hinrichs for the creation and release of these tracks. +</p> + +<!-- <a name="121525"></a> <h2>Dec. 15, 2025 New gnomAD Missense Deleteriousness Prediction by Constraint (MPC) track for hg19</h2> <p> We are happy to announce the release of the <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=ancient" target="_blank">Ancient Hominids track</a> featuring data from Archaic Sequence Hub (ArcSeqHub). This track shows variants identified by ArcSeqHub's remapping of high-quality Altai Neanderthal and Denisovan genomes onto the hg38/GRCh38 genome. Variants are divided into two subtracks, one for Denisovian variants and another for Neanderthal variants. UCSC has removed those positions from the VCF without an alternate allele to show only variants that are present in the ancient genomes.</p> <div class="text-center"> <img src="/images/newsArchImages/ancientHominids.png" width='80%'></a> </div> <p> We would like to thank the <a href="http://www.arcseqhub.com/plot/-1/" target="_blank">ArcSeqHub</a> authors for making the data available. We would also like to thank Maximilian Haeussler and Matthew Speir for the creation and release of this track.</p> - +--> <!-- <a name="120525"></a> <h2>Dec. 05, 2025 Hub Space: Host Your Track Hubs Directly on the Genome Browser</h2> <p> We are excited to introduce <a href="/cgi-bin/hgHubConnect#hubUpload">Hub Space</a>, a new hosting service that allows users to upload and visualize track hub files directly on the UCSC Genome Browser without relying on third-party hosting services such as Dropbox, Google Drive, or AWS. </p> <p> <b>Hub Space Features:</b><br> Each account is allocated 10 GB of storage space. While we strive to maintain uninterrupted access, please maintain your own backups. Data persistence over the long term is not