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<p class="MsoNormal"><span style="font-size:11.0pt;color:windowtext">Dr Cummins,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:windowtext"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:windowtext">I much appreciate your answer and elaboration of the history, which I was interested in.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:windowtext"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:windowtext">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:windowtext"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:windowtext">~Malcolm Cook<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:windowtext"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:windowtext"><o:p> </o:p></span></p>
<div style="border:none;border-left:solid blue 1.5pt;padding:0in 0in 0in 4.0pt">
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:11.0pt;color:windowtext">From:</span></b><span style="font-size:11.0pt;color:windowtext"> Carla Cummins <carlac@ebi.ac.uk>
<br>
<b>Sent:</b> Wednesday, May 22, 2019 5:57 AM<br>
<b>To:</b> Ensembl developers list <dev@ensembl.org>; Cook, Malcolm <MEC@stowers.org>; announce@ensembl.org; ensembl-campus@ebi.ac.uk; agall@ebi.ac.uk<br>
<b>Subject:</b> Re: [ensembl-dev] Ensembl 96 and Ensembl Genomes 43 are out!<o:p></o:p></span></p>
</div>
</div>
<div>
<p>Hi Malcolm,<o:p></o:p></p>
<p>Thank you for your question. I don't believe that there was an announcement regarding this alignment. Every time some new eligible species are included in Ensembl, they are automatically added to the relevant MSA. We consider this "business as usual" and
do not tend to make announcements about it. Apologies.<o:p></o:p></p>
<p>Regarding your other questions, the 25 fish alignment replaces an MSA with fewer fish species - previously 23. The current assembly of Mexican tetra has been a part of Ensembl - and therefore our alignments - since release 94 (Oct 2018). However, it was
previously referred to as 'Cave fish' rather than 'Mexican tetra', which is probably a little confusing. Prior to release 94, we had an earlier assembly, which has been present since late 2013. Below are some links to statistics on these fish alignments for
the previous few releases, to show the progression of this MSA:<o:p></o:p></p>
<p><a href="http://www.ensembl.org/info/genome/compara/mlss.html?mlss=1497">http://www.ensembl.org/info/genome/compara/mlss.html?mlss=1497</a><o:p></o:p></p>
<p><a href="http://jan2019.archive.ensembl.org/info/genome/compara/mlss.html?mlss=1371">http://jan2019.archive.ensembl.org/info/genome/compara/mlss.html?mlss=1371</a><o:p></o:p></p>
<p><a href="http://oct2018.archive.ensembl.org/info/genome/compara/mlss.html?mlss=1332">http://oct2018.archive.ensembl.org/info/genome/compara/mlss.html?mlss=1332</a><o:p></o:p></p>
<p><a href="http://jul2018.archive.ensembl.org/info/genome/compara/mlss.html?mlss=1133">http://jul2018.archive.ensembl.org/info/genome/compara/mlss.html?mlss=1133</a><o:p></o:p></p>
<p>I hope this helps,<o:p></o:p></p>
<p>Carla<o:p></o:p></p>
<p>---<br>
Dr Carla Cummins<br>
Ensembl Compara Developer<br>
EMBL-EBI, Wellcome Genome Campus<br>
Hinxton, Cambridge<br>
CB10 1SD<br>
United Kingdom<o:p></o:p></p>
<p><o:p> </o:p></p>
<div>
<p class="MsoNormal">On 21/05/2019 16:26, Cook, Malcolm wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"><span style="font-size:11.0pt">Hello,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I read at <a href="https://www.ensembl.org/info/genome/compara/mlss.html?mlss=1497">
25 fish EPO</a> that “This alignment has been generated in Ensembl release 96” </span>
<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Yet I see no mention of it in
</span><a href="http://www.ensembl.info/2019/04/09/ensembl-96-and-ensembl-genomes-43-are-out/">Ensembl 96 and Ensembl Genomes 43 are out!</a><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Is this perhaps:<o:p></o:p></p>
<ol style="margin-top:0in" start="1" type="a">
<li class="MsoListParagraph" style="margin-left:.25in;mso-list:l3 level1 lfo3">an oversight on your part<o:p></o:p></li><li class="MsoListParagraph" style="margin-left:.25in;mso-list:l3 level1 lfo3">or might the fish alignment be older that this<o:p></o:p></li><li class="MsoListParagraph" style="margin-left:.25in;mso-list:l3 level1 lfo3">or I should expect to find announcements re comparative genomics efforts elsewhere?<o:p></o:p></li><li class="MsoListParagraph" style="margin-left:.25in;mso-list:l3 level1 lfo3">Or am I otherwise misunderstanding how Ensembl is organized.<o:p></o:p></li></ol>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Also, is there anywhere an announcement for the alignment I might share among possibly interested colleagues, and is there anywhere a description of what it is replacing (if anything) (esp: was there a prior fish MSA that included Mexican
tetra?),<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Thanks very much,<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">~Malcolm Cook<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<div style="border:none;border-left:solid blue 1.5pt;padding:0in 0in 0in 4.0pt">
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<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:11.0pt">From:</span></b><span style="font-size:11.0pt"> Dev
<a href="mailto:dev-bounces@ensembl.org"><dev-bounces@ensembl.org></a> <b>On Behalf Of
</b>Astrid Gall<br>
<b>Sent:</b> Tuesday, April 9, 2019 7:01 AM<br>
<b>To:</b> <a href="mailto:dev@ensembl.org">dev@ensembl.org</a>; <a href="mailto:announce@ensembl.org">
announce@ensembl.org</a>; <a href="mailto:ensembl-campus@ebi.ac.uk">ensembl-campus@ebi.ac.uk</a><br>
<b>Subject:</b> [ensembl-dev] Ensembl 96 and Ensembl Genomes 43 are out!</span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-GB" style="font-family:"Arial",sans-serif;color:red">**CAUTION: Non-Stowers email**
</span><o:p></o:p></p>
<div>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">Dear all</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt"> </span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">We are pleased to announce that the latest Ensembl and Ensembl Genomes updates have been released:</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><a href="http://www.ensembl.org/"><span lang="EN-GB" style="font-size:12.0pt;color:#954F72">http://www.ensembl.org/</span></a><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><a href="http://ensemblgenomes.org/"><span lang="EN-GB" style="font-size:12.0pt;color:#1155CC">http://ensemblgenomes.org</span></a><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-GB"> </span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">Highlights of this release include:</span><o:p></o:p></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoNormal" style="mso-list:l1 level1 lfo6"><span lang="EN-GB">First-pass full annotation of the mouse genome (GENCODE M21 gene set)</span><o:p></o:p></li><li class="MsoNormal" style="mso-list:l1 level1 lfo6"><span lang="EN-GB">Release of Ensembl-RefSeq MANE Select v0.5 transcripts</span><o:p></o:p></li><li class="MsoNormal" style="mso-list:l1 level1 lfo6"><span lang="EN-GB">Update to GENCODE 30 for human</span><o:p></o:p></li><li class="MsoNormal" style="mso-list:l1 level1 lfo6"><span lang="EN-GB">Joint REST server for Ensembl and Ensembl Genomes</span><o:p></o:p></li><li class="MsoNormal" style="mso-list:l1 level1 lfo6"><span lang="EN-GB">Changes to FTP directory layout</span><o:p></o:p></li><li class="MsoNormal" style="mso-list:l1 level1 lfo6"><span lang="EN-GB">New genomes: 19 birds, five reptiles and 12 mammals</span><o:p></o:p></li><li class="MsoNormal" style="mso-list:l1 level1 lfo6"><span lang="EN-GB">New interface for configuration of regulation tracks</span><o:p></o:p></li></ul>
<p class="MsoNormal"><span lang="EN-GB"> </span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">The release blog post with all news can be viewed here:</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><a href="http://www.ensembl.info/2019/04/09/ensembl-96-and-ensembl-genomes-43-are-out/"><span lang="EN-GB" style="font-size:12.0pt">http://www.ensembl.info/2019/04/09/ensembl-96-and-ensembl-genomes-43-are-out/</span></a><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt"> </span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">For the latest news from the Ensembl project visit our blog at:</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><a href="http://www.ensembl.info/"><span lang="EN-GB" style="font-size:12.0pt;color:#954F72">http://www.ensembl.info</span></a><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt"> </span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">The release webinar is planned for Wednesday 17th April 2019 at 16:00 BST. Please register using the following URL:</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><a href="https://attendee.gototraining.com/r/8260823671959775489"><span lang="EN-GB" style="font-size:12.0pt;color:#1155CC">https://attendee.gototraining.com/r/8260823671959775489</span></a><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">Registration is free.</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt"> </span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">Best regards,</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt"> </span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">Astrid</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">On behalf of the Ensembl team</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">--</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">Dr Astrid Gall</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">Ensembl Outreach Officer</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI)</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">Wellcome Genome Campus</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">Hinxton, Cambridge</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">CB10 1SD</span><o:p></o:p></p>
<p style="margin:0in;margin-bottom:.0001pt"><span lang="EN-GB" style="font-size:12.0pt">United Kingdom</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-GB"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-GB"> </span><o:p></o:p></p>
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<pre>_______________________________________________<o:p></o:p></pre>
<pre>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><o:p></o:p></pre>
<pre>Posting guidelines and subscribe/unsubscribe info: <a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a><o:p></o:p></pre>
<pre>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></pre>
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<p class="MsoNormal"><span style="font-size:11.0pt">-- <br>
Carla Cummins, Ph.D.<br>
Ensembl Compara Developer<br>
European Bioinformatics Institute (EMBL-EBI),<br>
European Molecular Biology Laboratory,<br>
Wellcome Trust Genome Campus, Hinxton,<br>
Cambridge, CB10 1SD, United Kingdom<br>
Room A3-145<br>
Phone + 44 (0) 1223 49 4240<o:p></o:p></span></p>
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