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

Cook, Malcolm MEC at stowers.org
Tue May 21 17:26:12 BST 2019

Hello Ensemble Helpdesk and developers, again,

Helpdesk, I should have sent my earlier message to you in the first place.  Please read it below….

I do now see 48 fish EPO-Low-Coverage<https://www.ensembl.org/info/genome/compara/mlss.html?mlss=1404> which includes Mexican tetra.

I also see in Index of /pub/release-96/emf/ensembl-compara/multiple_alignments/25_fish.epo/<ftp://ftp.ensembl.org/pub/release-96/emf/ensembl-compara/multiple_alignments/25_fish.epo/> - that the files are dated 2/25/2019 so this MSA has been apparently available for a few months.

I still wonder if I missed an announcement somehow.


From: Dev <dev-bounces at ensembl.org> On Behalf Of Cook, Malcolm
Sent: Tuesday, May 21, 2019 10:27 AM
To: Ensembl developers list <dev at ensembl.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!


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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