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<p>Hi Malcolm,</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.</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:<br>
</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></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></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></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></p>
<p>I hope this helps,</p>
<p>Carla</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</p>
<p><br>
</p>
<span style="font-size:12.0pt;color:black" lang="EN-GB"></span>
<div class="moz-cite-prefix">On 21/05/2019 16:26, Cook, Malcolm
wrote:<br>
</div>
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<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt">Hello,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></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"
moz-do-not-send="true">
25 fish EPO</a> that “This alignment has been generated in
Ensembl release 96” <o:p>
</o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></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/"
moz-do-not-send="true">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:l2 level1 lfo4">an
oversight on your part<o:p></o:p></li>
<li class="MsoListParagraph"
style="margin-left:.25in;mso-list:l2 level1 lfo4">or might
the fish alignment be older that this<o:p></o:p></li>
<li class="MsoListParagraph"
style="margin-left:.25in;mso-list:l2 level1 lfo4">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:l2 level1 lfo4">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<span style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><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">From:</span></b><span
style="font-size:11.0pt"> Dev
<a class="moz-txt-link-rfc2396E" 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 class="moz-txt-link-abbreviated" href="mailto:dev@ensembl.org">dev@ensembl.org</a>; <a class="moz-txt-link-abbreviated" href="mailto:announce@ensembl.org">announce@ensembl.org</a>;
<a class="moz-txt-link-abbreviated" 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!<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span
style="font-family:"Arial",sans-serif;color:red"
lang="EN-GB">**CAUTION: Non-Stowers email**
</span><span style="font-size:11.0pt" lang="EN-GB"><o:p></o:p></span></p>
<div>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">Dear
all<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB"><o:p> </o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">We are
pleased to announce that the latest Ensembl and Ensembl
Genomes updates have been released:<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><a
href="http://www.ensembl.org/" moz-do-not-send="true"><span
style="font-size:12.0pt;color:#954F72" lang="EN-GB">http://www.ensembl.org/</span></a><span
style="font-size:12.0pt;color:black" lang="EN-GB"><o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><a
href="http://ensemblgenomes.org/" moz-do-not-send="true"><span
style="font-size:12.0pt;color:#1155CC" lang="EN-GB">http://ensemblgenomes.org</span></a><span
style="font-size:12.0pt;color:black" lang="EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black" lang="EN-GB"><o:p> </o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">Highlights
of this release include:<o:p></o:p></span></p>
<ul style="margin-top:0in" type="disc">
<li class="MsoNormal" style="color:black;mso-list:l0
level1 lfo3"><span lang="EN-GB">First-pass full
annotation of the mouse genome (GENCODE M21 gene set)<o:p></o:p></span></li>
<li class="MsoNormal" style="color:black;mso-list:l0
level1 lfo3"><span lang="EN-GB">Release of
Ensembl-RefSeq MANE Select v0.5 transcripts<o:p></o:p></span></li>
<li class="MsoNormal" style="color:black;mso-list:l0
level1 lfo3"><span lang="EN-GB">Update to GENCODE 30 for
human<o:p></o:p></span></li>
<li class="MsoNormal" style="color:black;mso-list:l0
level1 lfo3"><span lang="EN-GB">Joint REST server for
Ensembl and Ensembl Genomes<o:p></o:p></span></li>
<li class="MsoNormal" style="color:black;mso-list:l0
level1 lfo3"><span lang="EN-GB">Changes to FTP directory
layout<o:p></o:p></span></li>
<li class="MsoNormal" style="color:black;mso-list:l0
level1 lfo3"><span lang="EN-GB">New genomes: 19 birds,
five reptiles and 12 mammals<o:p></o:p></span></li>
<li class="MsoNormal" style="color:black;mso-list:l0
level1 lfo3"><span lang="EN-GB">New interface for
configuration of regulation tracks<o:p></o:p></span></li>
</ul>
<p class="MsoNormal"><span style="color:black" lang="EN-GB"><o:p> </o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">The
release blog post with all news can be viewed here:<o:p></o:p></span></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/"
moz-do-not-send="true"><span style="font-size:12.0pt"
lang="EN-GB">http://www.ensembl.info/2019/04/09/ensembl-96-and-ensembl-genomes-43-are-out/</span></a><span
style="font-size:12.0pt;color:black" lang="EN-GB"><o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB"><o:p> </o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">For
the latest news from the Ensembl project visit our blog
at:<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><a
href="http://www.ensembl.info/" moz-do-not-send="true"><span
style="font-size:12.0pt;color:#954F72" lang="EN-GB">http://www.ensembl.info</span></a><span
style="font-size:12.0pt;color:black" lang="EN-GB"><o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB"><o:p> </o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">The
release webinar is planned for Wednesday 17th April 2019
at 16:00 BST. Please register using the following URL:<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><a
href="https://attendee.gototraining.com/r/8260823671959775489"
moz-do-not-send="true"><span
style="font-size:12.0pt;color:#1155CC" lang="EN-GB">https://attendee.gototraining.com/r/8260823671959775489</span></a><span
style="font-size:12.0pt;color:black" lang="EN-GB"><o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">Registration
is free.<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB"><o:p> </o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">Best
regards,<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB"><o:p> </o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">Astrid<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">On
behalf of the Ensembl team<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">--<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">Dr
Astrid Gall<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">Ensembl
Outreach Officer<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">European
Molecular Biology Laboratory - European Bioinformatics
Institute (EMBL-EBI)<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">Wellcome
Genome Campus<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">Hinxton,
Cambridge<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">CB10
1SD<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span
style="font-size:12.0pt;color:black" lang="EN-GB">United
Kingdom<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span
lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
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<div class="moz-signature">-- <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</div>
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