c3bfc4b022d2fb4b343297bb880c974fe6d456de gperez2 Tue Mar 30 15:34:44 2021 -0700 News announcement for the updated mm39 chainNet track release, refs #26815 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index dfd7e8a..d999291 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,118 @@ <div class="col-sm-3"> <ul> <li><a href="#2005">2005 News</a></li> <li><a href="#2004">2004 News</a></li> <li><a href="#2003">2003 News</a></li> <li><a href="#2002">2002 News</a></li> <li><a href="#2001">2001 News</a></li> </ul> </div> </div> </div> <!-- ============= 2021 archived news ============= --> <a name="2021"></a> +<a name="033021"></a> +<h2>Mar. 30, 2021 Updated Chain/Net tracks for Mouse (mm39/GRCm39)</h2> +<p>We are pleased to announce the update to the <a target="_blank" +href="../../cgi-bin/hgTrackUi?db=mm39&g=mm39ChainNet&position=default">Chain/Net</a> tracks +for the recently released mouse assembly +<a target="_blank" href="../../cgi-bin/hgTracks?db=mm39" >mm39/GRCm39</a>. +The chain track shows alignments of the mouse assembly to 29 other +organisms using a gap scoring system that allows longer gaps than traditional affine gap scoring +systems. The net track shows the best mouse/other chain for every part of the other genome.</p><br> +<div class="container"> + <div class="row"> + <div class="col-sm-4"> + <ul> + <li>Bonobo <a href="../cgi-bin/hgTrackUi?db=panPan3&g=chainNetMm39&position=default" + target=_blank>(panPan3)</a></li> + <li>Bushbaby <a href="../cgi-bin/hgTrackUi?db=otoGar3&g=chainNetMm39&position=default" + target=_blank>(otoGar3)</a></li> + <li>Chicken <a href="../cgi-bin/hgTrackUi?db=galGal6&g=chainNetMm39&position=default" + target=_blank>(galGal6)</a></li> + <li>Chimp <a href="../cgi-bin/hgTrackUi?db=panTro6&g=chainNetMm39&position=default" + target=_blank>(panTro6)</a></li> + <li>Chinese pangolin <a href="../cgi-bin/hgTrackUi?db=manPen1&g=chainNetMm39&position=default" + target=_blank>(manPen1)</a></li> + <li>Cow <a href="../cgi-bin/hgTrackUi?db=bosTau9&g=chainNetMm39&position=default" + target=_blank>(bosTau9)</a></li> + <li>Dolphin <a href="../cgi-bin/hgTrackUi?db=turTru2&g=chainNetMm39&position=default" + target=_blank>(turTru2)</a></li> + <li>Elephant <a href="../cgi-bin/hgTrackUi?db=loxAfr3&g=chainNetMm39&position=default" + target=_blank>(loxAfr3)</a></li> + <li>Gorilla <a href="../cgi-bin/hgTrackUi?db=gorGor6&g=chainNetMm39&position=default" + target=_blank>(gorGor6)</a></li> + <li>Guinea pig <a href="../cgi-bin/hgTrackUi?db=cavPor3&g=chainNetMm39&position=default" + target=_blank>(cavPor3)</a></li> + </ul> + </div> + <div class="col-sm-4"> + <ul> + <li>Hawaiian monk seal <a href="../cgi-bin/hgTrackUi?db=neoSch1&g=chainNetMm39&position=default" + target=_blank>(neoSch1)</a></li> + <li>Hedgehog <a href="../cgi-bin/hgTrackUi?db=eriEur2&g=chainNetMm39&position=default" + target=_blank>(eriEur2)</a></li> + <li>Horse <a href="../cgi-bin/hgTrackUi?db=equCab3&g=chainNetMm39&position=default" + target=_blank>(equCab3)</a></li> + <li>Lamprey <a href="../cgi-bin/hgTrackUi?db=petMar3&g=chainNetMm39&position=default" + target=_blank>(petMar3)</a></li> + <li>Malayan flying lemur <a href="../cgi-bin/hgTrackUi?db=galVar1&g=chainNetMm39&position=default" + target=_blank>(galVar1)</a></li> + <li>Opossum <a href="../cgi-bin/hgTrackUi?db=monDom5&g=chainNetMm39&position=default" + target=_blank>(monDom5)</a></li> + <li>Pig <a href="../cgi-bin/hgTrackUi?db=susScr3&g=chainNetMm39&position=default" + target=_blank>(susScr3)</a></li> + <li>Pika <a href="../cgi-bin/hgTrackUi?db=ochPri3&g=chainNetMm39&position=default" + target=_blank>(ochPri3)</a></li> + <li>Rabbit <a href="../cgi-bin/hgTrackUi?db=oryCun2&g=chainNetMm39&position=default" + target=_blank>(oryCun2)</a></li> + <li>Rat <a href="../cgi-bin/hgTrackUi?db=rn6&g=chainNetMm39&position=default" + target=_blank>(rn6)</a></li> + </ul> + </div> + <div class="col-sm-4"> + <ul> + <li>Rhesus <a href="../cgi-bin/hgTrackUi?db=rheMac10&g=chainNetMm39&position=default" + target=_blank>(rheMac10)</a></li> + <li>Sheep <a href="../cgi-bin/hgTrackUi?db=oviAri4&g=chainNetMm39&position=default" + target=_blank>(oviAri4)</a></li> + <li>Shrew <a href="../cgi-bin/hgTrackUi?db=sorAra2&g=chainNetMm39&position=default" + target=_blank>(sorAra2)</a></li> + <li>Squirrel <a href="../cgi-bin/hgTrackUi?db=speTri2&g=chainNetMm39&position=default" + target=_blank>(speTri2)</a></li> + <li>Tarsier <a href="../cgi-bin/hgTrackUi?db=tarSyr2&g=chainNetMm39&position=default" + target=_blank>(tarSyr2)</a></li> + <li>Tenrec <a href="../cgi-bin/hgTrackUi?db=echTel2&g=chainNetMm39&position=default" + target=_blank>(echTel2)</a></li> + <li>Tree shrew <a href="../cgi-bin/hgTrackUi?db=tupBel1&g=chainNetMm39&position=default" + target=_blank>(tupBel1)</a></li> + <li>X. tropicalis <a href="../cgi-bin/hgTrackUi?db=xenTro9&g=chainNetMm39&position=default" + target=_blank>(xenTro9)</a></li> + <li>Zebrafish <a href="../cgi-bin/hgTrackUi?db=danRer11&g=chainNetMm39&position=default" + target=_blank>(danRer11)</a></li> + </ul> + </div> + </div> +</div> + +<p> +We would like to thank Angie Hinrichs, Hiram Clawson, Lou Nassar, and Gerardo Perez for the +development and release of this track.</p> + <a name="032321"></a> <h2>Mar. 23, 2020 New GENCODE gene tracks: Human V37 (hg19/hg38) - Mouse M26 (mm39)</h2> <p> We are pleased to announce new GENCODE Gene annotation tracks, which correspond to <a href="https://www.ensembl.info/2021/02/15/ensembl-103-has-been-released/" target="_blank">Ensembl 103</a>, for three assemblies: <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgEncodeGencodeV37lift37">hg19/GRCh37</a>, <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38&c=chr1&g=wgEncodeGencodeV37">hg38/GRCh38</a>, and <a target="_blank" href="../../cgi-bin/hgTrackUi?db=mm39&c=chr12&g=wgEncodeGencodeVM26">mm39/GRCm39</a>. For human, the GENCODE V37 annotations were mapped to hg38/GRCh38 and then back-mapped to the hg19/GRCh37 assembly. For all three assemblies, the gene sets contain the following tracks:</p> <ul> <li>Basic - a subset of the <em>Comprehensive set</em>.</li>