8cd99720275c9d69502aade7523349b92edf278b lrnassar Thu Nov 30 10:29:32 2023 -0800 News announcement for the HGVS search feature, refs #26016 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index ee73c25..876172d 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,30 +51,68 @@ </div> <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 <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 <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>our GitHub page</a>.</p> <!-- ============= 2023 archived news ============= --> <a name="2023"></a> +<a name="113023"></a> +<h2>Nov. 30, 2023 Support for previous RefSeq transcripts while searching on hg38</h2> +<p> +Have you ever found a variant in a paper and searched for it on the Genome Browser only +to receive an error that the sequence cannot be found? Or perhaps looked up a familiar +NM_ identifier and suddenly found no results?</p> +<p> +We are pleased to share that we now have support for searching previous RefSeq +transcript versions on hg38. This support works for both NM_ accessions +and <a target="_blank" href="https://hgvs-nomenclature.org/en/latest/">HGVS</a> +searching as demonstrated below:</p> + +<p> +<b>Searching for the latest transcript which always worked:</b> +<ul> +<li> +Sequence search: <a target="_blank" +href="../cgi-bin/hgSearch?search=NM_198056.3&db=hg38">NM_198056.3</a></li> +<li> +HGVS search: <a target="_blank" +href="../cgi-bin/hgSearch?search=NM_198056.3%3Ac.1A%3EC&db=hg38">NM_198056.3:c.1A>C</a></li></ul></p> +<p> +<b>Searching for a previous version that now works::</b> +<ul> +<li> +Sequence search: <a target="_blank" +href="../cgi-bin/hgSearch?search=NM_198056.3&db=hg38">NM_198056.2</a></li> +<li> +HGVS search: <a target="_blank" +href="../cgi-bin/hgSearch?search=NM_198056.3%3Ac.1A%3EC&db=hg38">NM_198056.2:c.1A>C</a></li></ul></p> + +<p> +We thank <a target="_blank" href="https://www.ncbi.nlm.nih.gov/">NCBI</a> and Terence +Murphy for creating the archive of deprecated transcripts that allows this feature +to work. We would also like to thank the users who wrote requesting the feature +allowing us to prioritize it effectively. Finally, we would like to thank Chris Lee, +Max Haeussler, Gerardo Perez, and Lou Nassar for developing and testing this feature.</p> + <a name="112223"></a> <h2>Nov. 22, 2023 CRISPR Targets for Zebrafish (danRer10/danRer11) now available</h2> <p> We are happy to announce the release of the CRISPR Targets track for the Zebrafish <a href="../cgi-bin/hgTrackUi?db=danRer10&g=crisprAllTargets" target="_blank">danRer10</a> and <a href="../cgi-bin/hgTrackUi?db=danRer11&g=crisprAllTargets" target="_blank">danRer11</a> assemblies. CRISPR-Cas9 has been applied in Zebrafish for gene knockout, gene screening and other gene editing studies.</p> <p> The CRISPR Targets track shows the DNA sequences targetable by CRISPR RNA guides using the Cas9 enzyme from S. pyogenes (PAM: NGG) over the entire zebrafish genome. CRISPR target sites were annotated with predicted specificity (off-target effects) and predicted efficiency (on-target cleavage) by various algorithms through the tool <a href="http://crispor.tefor.net/" target="_blank">CRISPOR</a>. The target sequence of the guide is shown with a thick (exon) bar. The PAM motif match (NGG) is shown with a thinner bar. Guides are