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...

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.

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...

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.

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

Please take our user survey!

We're surveying our users to find out more about what you use Ensembl Genomes for, what we do well and what we could do better. The survey should take up only a few minutes of your time, and your answers will be very useful to us: please follow the link to participate https://www.surveymonkey.com/s/HV5T5HZ and feel free to share the link with other users of our service. Thank you!

posted 2015-05-06
Job opportunity with WormBase-ParaSite
Our sister project, WormBase-ParaSite, uses Ensembl infrastructure to provide early access to data from pathogenic worms. We are seeking to hire a bioinformatician to work on this project, based at the Wellcome Trust Sanger Institute. Click here for more details.
posted 2015-04-20
Decommissioning of Sequence Search service

Hitherto, Ensembl Genomes has made two alternative sequence searches available, one operated by the European Nucleotide Archive (and available through the link 'Sequence Search' in the header of Ensembl Genomes sites), and one using BLAST. The ENA-provided search will be decommissioned for all divisions with the release of Ensembl Genomes 27, currently planned for the end of May. The BLAST service will remain available for all divisions (metazoa, plants, fungi, protists and bacteria).

posted 2015-04-15
MySQL database retention policy

As the amount of data in each release of Ensembl Genomes increases, it has become necessary to restrict the number of past releases available on our public MySQL server (mysql-eg-publicsql.ebi.ac.uk).

Shortly before the release 27 of Ensembl Genomes in June 2015, all databases from all releases prior to release 18 will be removed. With each subsequent release, data from the oldest release will be removed at release time, leaving data from the most recent 10 releases only. The removal of each release will be announced with the intentions for the new release approximately 2 months in advance.

Please note that the data available from our FTP site will be unaffected by this change in policy, with data from all releases of Ensembl Genomes remaining available in all supported formats, including full MySQL dumps.

posted 2015-03-25
Future releases

Release 27 of Ensembl Genomes is scheduled for 26th May 2015 - more details in Ensembl Genomes Release 27 Intentions.

posted 2014-08-22
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

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 26 (March 2015)

The 26th release of Ensembl Genomes features updates to version 79 of the Ensembl software across all divisions, and a number of new genomes bringing the total number of genomes to 20,890 (full list). Detailed notes can be found here. See the individual homepages for more information.

Ensembl Bacteria has been updated to include the latest versions of 21,767 genomes (21,479 bacteria and 289 archaea) from the INSDC archives.

This release of Ensembl Fungi contains new variation data for the plant pathogens Verticillium dahliae JR2 and Zymoseptoria tritici.

Community-annotated gene names and descriptions have been added for the centipede, Strigamia maritima.

This release of Ensembl Plants includes the latest genome and annotation assembly of Medicago truncatula from the Medicago truncatula Sequencing Consortium (read more). Additionally, seven new whole genome alignments between the Triticeae genomes using the ATAC aligner have been included, including alignments between the Triticum aestivum (bread wheat) component genomes (A, B and D stats), Triticum urartu against the bread wheat A genome (stats), Aegilops tauschii against the bread wheat D genome (stats), Triticum urartu against Aegilops tauschii (stats), and Hordeum vulgare against Triticum aestivum (stats), Triticum urartu (stats) and Aegilops tauschii (stats).

No significant changes have been made to Ensembl Protists for this release.

Release notes from previous releases