In collaboration with the Ecole Normale Superieure, Paris and the J. Craig Venter Institute, San Diego, we have re-annotated the genome of the marine diatom Phaeodactylum tricornutum. The new annotation was produced using 13,828 non-redundant ESTs, 42 libraries of RNA-Seq generated using Illumina technology and 49 libraries of RNA-Seq data generated under various iron conditions using SoLiD technology, as well as gene models previously predicted in this and related species. The new gene set contains a total of 12,089 protein coding genes, an increase from the 10,402 genes previously predicted. Models have been checked and corrected through a process of manual curation. The gene models have been analysed using InterProScan and Ensembl Compara and are available to explore in Ensembl Protists.

Three new variation data sets for Hordeum vulgare (barley) are included in this release. Two are from recent population sequencing (POPSEQ) experiments: ~5 million variant calls from POPSEQ of cv. Morex x cv. Barke progeny, over 6 million variant calls from POPSEQ of Oregon Wolfe barley. In addition, around 7,000 iSelect SNPs, mapped to ~2,600 iSelect markers have been added. These, and all other barley variations, have been accessioned in the transPLANT variation archive. Read more...

This release of Ensembl Plants includes an ordered version of the IWGSC genome assembly for Triticum aestivum (bread wheat). The existing Chromosome Survey Sequence (CSS) contigs were ordered using POPSEQ data from IPK Gatersleben. Additionally, the IWGSC's BAC by BAC assembly and annotation of chromosome 3B replaces the CSS-derived assembly of 3B. Read more...

Following the launch of the new ncRNA sequence resource RNAcentral, Ensembl Genomes can now show alignments of sequences in RNAcentral against selected genomes. Turn on the "RNAcentral" track using the "Genes and transcripts" configuration menu, or try an example.

The latest Drosophila melanogaster assembly (BDGP6) is in Ensembl Metazoa, and pairwise alignments to other dipterans have been generated.

We are hiring!

We are currently seeking to hire software engineers, bioinformaticians and web developers to help develop our services. Please take a look as the links and either apply or contact pkersey AT ebi DOT ac DOT uk if you have any questions.

posted 2015-01-07
New REST server

The REST server provided by Ensembl Genomes has now been updated to use the latest v3.0.0 codebase provided by Ensembl, plus supplementary endpoints for genome discovery and bacterial family/genome retrieval. For more information on these additional endpoints, please visit:
https://github.com/EnsemblGenomes/eg-rest/wiki/

The new server is available at http://rest.ensemblgenomes.org/ - please note that http://beta.ensemblgenomes.org will remain accessible until the next release of Ensembl Genomes in October after which point it will be removed.

posted 2014-08-20
New public MySQL server

The Ensembl Genomes public MySQL server is now located on mysql-eg-publicsql.ebi.ac.uk, port 4157. Please update your scripts to use this new location.

mysql.ebi.ac.uk port 4157 will be retired on 4th December 2014

posted 2014-08-19

Future releases

Release 26 of Ensembl Genomes is scheduled for 17th March 2015. For more details, see the release intentions.

Ensembl Genomes is developed by EMBL-EBI and is powered by Ensembl software system for the analysis and visualisation of genomic data. For details of our funding please click here.

Have a question?

Frequently Asked Questions (FAQs) are now available for all domains of Ensembl Genomes. Have a question? Check if it's been asked before! If there is a FAQ missing, contact us.

What's New in Release 25 (January 2015)

Ensembl Bacteria has been updated to include the latest versions of 20,995 genomes (20,710 bacteria and 286 archaea) from the INSDC archives.

This release of Ensembl Fungi sees new data for two important plant pathogens. There is a new assembly and gene build for Fusarium graminearum (Gibberella zeae), and a genome for the JR2 strain of Verticillium dahliae. In addition, new cross-references to PHI-base have been loaded, with increased annotation in particular for Magnaporthe oryzae. Finally, a number of species have been renamed in line with community policy: members of the Fusarium genus have been renamed as per Geisser et al., 2013; Botryotinia fuckeliana to Botrytis cinerea; and Glomerella graminicola to Colletotrichum graminicola.

The latest assembly version (BDGP6) of Drosophila melanogaster has been included, as has the latest D. pseudoobscura assembly (v3.0). Annotation and cross-references for other drosophilids were also updated. The new D. melanogaster assembly prompted new pairwise whole genome alignments between fruit fly and all other dipterans in Ensembl Metazoa. And finally, in this model-organism-themed release, the Caenorhabditis elegans gene set was updated to WormBase version WS245.

This release of Ensembl Plants includes an ordered version of the IWGSC genome assembly for Triticum aestivum (bread wheat). The existing Chromosome Survey Sequence (CSS) contigs were ordered using POPSEQ data from IPK Gatersleben. Additionally, the IWGSC's BAC by BAC assembly and annotation of chromosome 3B replaces the CSS-derived assembly of 3B. Read more...

New variation and marker data have been added to Hordeum vulgare (barley). This includes nearly 7,000 iSelect SNPs mapped to ~2,600 iSelect markers, and more than 10 million POPSEQ variations from two mapping populations. Read more...

New whole genome alignments between Brassica rapa (A) and Brassica oleracea (C) have been produced (see a summary), and can be viewed in the browser.

A new genebuild is available for the marine diatom Phaeodactylum tricornutum, produced by Ensembl Genomes in collaboration with the Ecole Normale Superieure, Paris and the J. Craig Venter Institute, San Diego, and combining existing gene models with new EST and RNAseq data.

Release notes from previous releases