[ensembl-dev] Ensembl 96 and Ensembl Genomes 43 are out!

Cook, Malcolm MEC at stowers.org
Wed May 22 17:20:30 BST 2019

Dr Cummins,

I much appreciate your answer and elaboration of the history, which I was interested in.


~Malcolm Cook

From: Carla Cummins <carlac at ebi.ac.uk>
Sent: Wednesday, May 22, 2019 5:57 AM
To: Ensembl developers list <dev at ensembl.org>; Cook, Malcolm <MEC at stowers.org>; announce at ensembl.org; ensembl-campus at ebi.ac.uk; agall at ebi.ac.uk
Subject: Re: [ensembl-dev] Ensembl 96 and Ensembl Genomes 43 are out!

Hi Malcolm,

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.

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:





I hope this helps,


Dr Carla Cummins
Ensembl Compara Developer
EMBL-EBI, Wellcome Genome Campus
Hinxton, Cambridge
CB10 1SD
United Kingdom

On 21/05/2019 16:26, Cook, Malcolm wrote:

I read at 25 fish EPO<https://www.ensembl.org/info/genome/compara/mlss.html?mlss=1497> that “This alignment has been generated in Ensembl release 96”

Yet I see no mention of it in Ensembl 96 and Ensembl Genomes 43 are out!<http://www.ensembl.info/2019/04/09/ensembl-96-and-ensembl-genomes-43-are-out/>

Is this perhaps:

  1.  an oversight on your part
  2.  or might the fish alignment be older that this
  3.  or I should expect to find announcements re comparative genomics efforts elsewhere?
  4.  Or am I otherwise misunderstanding how Ensembl is organized.

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?),

Thanks very much,

~Malcolm Cook

From: Dev <dev-bounces at ensembl.org><mailto:dev-bounces at ensembl.org> On Behalf Of Astrid Gall
Sent: Tuesday, April 9, 2019 7:01 AM
To: dev at ensembl.org<mailto:dev at ensembl.org>; announce at ensembl.org<mailto:announce at ensembl.org>; ensembl-campus at ebi.ac.uk<mailto:ensembl-campus at ebi.ac.uk>
Subject: [ensembl-dev] Ensembl 96 and Ensembl Genomes 43 are out!

**CAUTION: Non-Stowers email**

Dear all

We are pleased to announce that the latest Ensembl and Ensembl Genomes updates have been released:



Highlights of this release include:

  *   First-pass full annotation of the mouse genome (GENCODE M21 gene set)
  *   Release of Ensembl-RefSeq MANE Select v0.5 transcripts
  *   Update to GENCODE 30 for human
  *   Joint REST server for Ensembl and Ensembl Genomes
  *   Changes to FTP directory layout
  *   New genomes: 19 birds, five reptiles and 12 mammals
  *   New interface for configuration of regulation tracks

The release blog post with all news can be viewed here:


For the latest news from the Ensembl project visit our blog at:


The release webinar is planned for Wednesday 17th April 2019 at 16:00 BST. Please register using the following URL:


Registration is free.

Best regards,


On behalf of the Ensembl team


Dr Astrid Gall

Ensembl Outreach Officer

European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI)

Wellcome Genome Campus

Hinxton, Cambridge

CB10 1SD

United Kingdom


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Carla Cummins, Ph.D.
Ensembl Compara Developer
European Bioinformatics Institute (EMBL-EBI),
European Molecular Biology Laboratory,
Wellcome Trust Genome Campus, Hinxton,
Cambridge, CB10 1SD, United Kingdom
Room A3-145
Phone + 44 (0) 1223 49 4240
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