EnsemblGenomes and Ensembl REST services merged

This announcement from Ensembl


includes the merger of these REST service endpoints.

This states that rest.ensemblgenomes.org has been retired, although as of today it is still responding.

Before it is retired (i.e. now), Jalview users need to be advised to add this line to their .jalview_properties file in order to fetch ‘EnsemblGenomes’ accessions:


Jalview should then be ‘tidied up’ (code and documentation) to better reflect the merger of these services, however this is not urgent given the above workaround. Issue is JAL-3193.


The University of Dundee is a registered Scottish Charity, No: SC015096


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Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK



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From: Announce announce-bounces@ensembl.org on behalf of announce-request@ensembl.org announce-request@ensembl.org
Sent: 10 April 2019 12:00
To: announce@ensembl.org
Subject: Announce Digest, Vol 1, Issue 1

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Today’s Topics:

  1. Ensembl 96 and Ensembl Genomes 43 are out! (Astrid Gall)

Message: 1
Date: Tue, 09 Apr 2019 13:01:18 +0100
From: Astrid Gall agall@ebi.ac.uk
To: dev@ensembl.org, announce@ensembl.org,
Subject: [ensembl-announce] Ensembl 96 and Ensembl Genomes 43 are out!
Message-ID: 20190409120152.8134962BFE7_CAC89B0B@hh-mx3.ebi.ac.uk
Content-Type: text/plain; charset=“utf-8”

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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