79b493d56edd2ffdafebdd20bc69528b3bdfee0a lrnassar Mon Sep 28 15:54:54 2026 -0700 News announcement for the redesigned BLAT search and results pages, with the matching indexNews.html item. The entry carries two anchors: #100726 for the usual date form and #newBLAT, which the blatNewFormNewsUrl hg.conf setting on the BLAT banner points at. The banner announces the switch to the new pages on October 28. refs #37996 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 7c0a1336af5..b4089c6ceac 100644 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,88 @@ <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> <!-- ============= 2026 archived news ============= --> <a name="2026"></a> +<a name="newBLAT"></a> +<a name="100726"></a> +<h2>Oct. 7, 2026 Redesigned BLAT search and results pages</h2> +<p> +We are happy to announce a redesign of our +<a href="/cgi-bin/hgBlat" target="_blank">BLAT</a> sequence search tool. You can +reach the new pages from the banner on the current BLAT pages now, and they will +become the default on <b>October 28</b>. You will be able to opt out of the new page +and continue to use the classic interface after the change. +</p> + +<h3>Summary of changes</h3> +<ul> + <li> + A single search box lets you find any of our assemblies, including the more than + 5,000 GenArk assembly hubs, by typing a species name, common name, or accession. + Below it you will find quick picks for your recent assemblies, tabs to paste a + sequence or upload a file, a live character counter, and a link listing the input + limits. + </li> + <li> + Results now appear in a sortable, filterable table instead of the fixed-width text + output. Each hit shows a query coverage bar, score, identity, and span, and + clicking a row opens a panel with links to view the hit in the Genome Browser or + inspect the base-by-base alignment on a redesigned alignment page. + </li> + <li> + Each hit now also shows its gene locus, one of our most requested features, so you + can see which gene a match falls in without opening it in the Genome Browser. + </li> + <li> + From the results page you can also rename the BLAT results track, display your + query sequence, and share your results with a stable link that keeps the result + available to colleagues for 48 hours. + </li> + <li> + Result tracks now have their own <b>BLAT Results</b> group on the main browser + page and in the track search, separate from Custom Tracks, with a button to delete + all of them at once. + </li> + <li> + The tracks have clearer names, made of the query size and the gene at the top hit, + for example "360bp SOD1", instead of "blat YourSeq". + </li> + <li> + We have added a new option, <b>Keep only last search</b>, that will keep only your + latest results and discard the previous ones. This behavior will match how BLAT + has previously worked. + </li> +</ul> + +<p> +If you have feedback on the new pages, we would love to hear from you at +<a href="/contacts.html" target="_blank">our contact page</a>. +We would like to thank Maximilian Haeussler, Lou Nassar, Gerardo Perez, Brian Raney, +and the entire QA team for the design, development, and testing of these features. +</p> + <a name="091026"></a> <h2>Sep. 10, 2026 New AlphaGenome Variant Impact (AVI) score track for hg38</h2> <p> We are pleased to announce a new track showing the <a href="/cgi-bin/hgTrackUi?db=hg38&g=alphaGenome&position=default" target="_blank">AlphaGenome Variant Impact (AVI) score</a> from Google DeepMind's AlphaGenome Atlas, on the human GRCh38/hg38 assembly. The score combines AlphaGenome's predictions of how a variant affects gene regulation, covering expression, splicing, chromatin accessibility and transcription factor binding across hundreds of cell types, with AlphaMissense predictions for protein-altering changes. The result is a single number that ranks how damaging a substitution is likely to be. Unlike most prediction scores, it covers non-coding variants as well as coding ones, across the whole genome. </p> <div class="text-center" style="margin-top: 1.5em;"> <a href="https://genome.ucsc.edu/s/Lou/AlphaGenome" target="_blank">