f7efb7d4b2dd13e10e539c6be58501786d5b3aa5 lrnassar Wed Jul 24 17:16:41 2024 -0700 News announcement for evaSnp 6 tracks, refs #34119 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 3ff19a5..388b90b 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -54,30 +54,167 @@ <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> <!-- ============= 2024 archived news ============= --> <a name="2024"></a> +<a name="072524"></a> +<h2>Jul. 25, 2024 EVA SNP release 6 for 37 assemblies</h2> +<p> +We are pleased to announce the release of the EVA SNP release 6 track for 37 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 6. The full list of +assemblies that contain the EVA SNP release 6 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=evaSnp4" + target="_blank">(anoGam3)</a></li> + <li>C. intestinalis <a href="../cgi-bin/hgTrackUi?db=ci3&g=evaSnp4" + target="_blank">(ci3)</a></li> + <li>Bison <a href="../cgi-bin/hgTrackUi?db=bisBis1&g=evaSnp4" + target="_blank">(ci3)</a></li> + <li>Cat <a href="../cgi-bin/hgTrackUi?db=felCat8&g=evaSnp4" + target="_blank">(felCat8)</a>, + <a href="../cgi-bin/hgTrackUi?db=felCat9&g=evaSnp4" + target="_blank">(felCat9)</a></li> + <li>Chicken <a href="../cgi-bin/hgTrackUi?db=galGal4&g=evaSnp4" + target="_blank">(galGal4)</a>, + <a href="../cgi-bin/hgTrackUi?db=galGal5&g=evaSnp4" + target="_blank">(galGal5)</a>, + <a href="../cgi-bin/hgTrackUi?db=galGal6&g=evaSnp4" + target="_blank">(galGal6)</a></li> + <li>Chimp <a href="../cgi-bin/hgTrackUi?db=panTro4&g=evaSnp4" + target="_blank">(panTro4)</a>, + <a href="../cgi-bin/hgTrackUi?db=panTro5&g=evaSnp4" + target="_blank">(panTro5)</a></li></li> + <li>Cow <a href="../cgi-bin/hgTrackUi?db=bosTau7&g=evaSnp4" + target="_blank">(bosTau7)</a> + <li>Crab-eating macaque <a href="../cgi-bin/hgTrackUi?db=macFas5&g=evaSnp4" + target="_blank">(macFas5)</a></li> + <li>D. melanogaster <a href="../cgi-bin/hgTrackUi?db=dm6&g=evaSnp4" + target="_blank">(dm6)</a></li> + </ul></div> + <div class="col-sm-4"> + <ul> + <li>Dog <a href="../cgi-bin/hgTrackUi?db=canFam3&g=evaSnp4" + target="_blank">(canFam3)</a></li> + <li>Gorilla <a href="../cgi-bin/hgTrackUi?db=gorGor3&g=evaSnp4" + target="_blank">(gorGor3)</a>, + <a href="../cgi-bin/hgTrackUi?db=gorGor4&g=evaSnp4" + target="_blank">(gorGor4)</a></li> + <li>Green monkey <a href="../cgi-bin/hgTrackUi?db=chlSab2&g=evaSnp4" + target="_blank">(chlSab2)</a></li> + <li>Horse <a href="../cgi-bin/hgTrackUi?db=equCab3&g=evaSnp4" + target="_blank">(equCab3)</a></li> + <li>Marmoset <a href="../cgi-bin/hgTrackUi?db=calJac3&g=evaSnp4" + target="_blank">(calJac3)</a></li> + <li>Mouse <a href="../cgi-bin/hgTrackUi?db=mm10&g=evaSnp4" + target="_blank">(mm10)</a>, + <a href="../cgi-bin/hgTrackUi?db=mm39&g=evaSnp4" + target="_blank">(mm39)</a></li> + <li>Nile tilapia <a href="../cgi-bin/hgTrackUi?db=oreNil2&g=evaSnp4" + target="_blank">(oreNil2)</a></li> + <li>Orangutan <a href="../cgi-bin/hgTrackUi?db=ponAbe3&g=evaSnp4" + target="_blank">(ponAbe3)</a></li> + </ul></div> + <div class="col-sm-4"> + <ul> + <li>Pig <a href="../cgi-bin/hgTrackUi?db=susScr11&g=evaSnp4" + target="_blank">(susScr11)</a>, + <a href="../cgi-bin/hgTrackUi?db=susScr3&g=evaSnp4" + target="_blank">(susScr3)</a></li> + <li>Rat <a href="../cgi-bin/hgTrackUi?db=rn5&g=evaSnp4" + target="_blank">(rn5)</a>, + <a href="../cgi-bin/hgTrackUi?db=rn7&g=evaSnp4" + target="_blank">(rn7)</a></li> + <li>Rhesus <a href="../cgi-bin/hgTrackUi?db=rheMac10&g=evaSnp4" + target="_blank">(rheMac10)</a>, + <a href="../cgi-bin/hgTrackUi?db=rheMac8&g=evaSnp4" + target="_blank">(rheMac8)</a></li> + <li>S. cerevisiae <a href="../cgi-bin/hgTrackUi?db=sacCer3&g=evaSnp4" + target="_blank">(ponAbe3)</a></li> + <li>Sheep <a href="../cgi-bin/hgTrackUi?db=oviAri3&g=evaSnp4" + target="_blank">(oviAri3)</a>, + <a href="../cgi-bin/hgTrackUi?db=oviAri4&g=evaSnp4" + target="_blank">(oviAri4)</a></li> + <li>Turkey <a href="../cgi-bin/hgTrackUi?db=melGal5&g=evaSnp4" + target="_blank">(melGal5)</a></li> + <li>Zebra finch <a href="../cgi-bin/hgTrackUi?db=taeGut2&g=evaSnp4" + target="_blank">(taeGut2)</a></li> + <li>Zebrafish <a href="../cgi-bin/hgTrackUi?db=danRer7&g=evaSnp4" + target="_blank">(danRer7)</a>, + <a href="../cgi-bin/hgTrackUi?db=danRer10&g=evaSnp4" + target="_blank">(danRer10)</a>, + <a href="../cgi-bin/hgTrackUi?db=danRer11&g=evaSnp4" + 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 is 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 + maybe be represented as Ref = GA and Alt = G. + <li> <b>insertion</b> — + One or more nucleotides is 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 maybe + be represented as Ref = G and Alt = GT + <li> <b>delins</b> — + Similar to tandemRepeat, 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 track description page.</p> + +<p> +We would like to thank the <a href="https://www.ebi.ac.uk/eva/" target="_blank">European Variation +Archive</a> making this data publically available. We would also like to thank Luis Nassar, Chris Lee, +and Angie Hinrichs for the creation and release of these tracks. +</p> + <a name="071224"></a> <h2>Jul. 12, 2024 First update to hg19's UCSC Genes track since 2013</h2> <p> The UCSC Genome Browser is getting ready to update hg19's UCSC Genes dataset for the first time since 2013. In this update, the UCSC Genes track will now use GENCODE v45 gene models lifted to hg19 and replace the old UCSC transcript IDs with the official GENCODE IDs. </p> <p> The anticipated release date for this update is July 31, 2024.</p> <p> As an example of what to expect, here are some GENCODE IDs that will replace the UCSC IDs in the update:</p> <pre>