35a8919fea29ca7881ea71382065bddaf5152e68 gperez2 Wed Nov 22 14:45:36 2023 -0800 Announcing crispr tracks for danRer10 and danRer11, refs #21863 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 9743a99..ee73c25 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,30 +51,54 @@ </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="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 +colored to reflect both predicted specificity and efficiency. Specificity reflects the "uniqueness" +of a 20mer sequence in the genome; the less unique a sequence is, the more likely it is to cleave +other locations of the genome (off-target effects). Efficiency is the frequency of cleavage at the +target site (on-target efficiency).</p> +<p> +We would like to thank Maximilian Haeussler, Hiram Clawson, and Gerardo Perez for developing and +releasing these tracks.</p> + + <a name="110823"></a> <h2>Nov. 08, 2023 New track decorators feature</h2> <p> We are excited to introduce the new track decorators feature which allows highlighting parts of features with colors and/or symbols (glyphs/shapes) within a single track. </p> <div class="text-center"> <a href="http://genome.ucsc.edu/s/gperez2/RM_32467" target="_blank"> <img src="../images/newsArchImages/feature_decorators.png" style="width:80%;max-width:1083px"></a> </div> <p> The genome browser‘s primary way to annotate the genome uses colored rectangles (“exons” for gene tracks) linked by thin lines (“introns”), often stored as a bigBed. These were originally used for genes but then evolved to cover other types of annotations, e.g. enhancers, chromatin modifications, or single nucleotide variants. We usually