Ensembl Genomes

The Ensembl Genomes project produces genome databases for important species from across the taxonomic range, using the Ensembl software system. Five sites are now available: the existing Ensembl Bacteria, Ensembl Protists and Ensembl Metazoa sites plus the newly released Ensembl Plants and Ensembl Fungi sites. These new sites complement the existing Ensembl site, with its focus on vertebrate genomes. You can search all Ensembl and Ensembl Genomes databases from the search bar in the top right of this page.

Ensembl Genomes data is available through many of the same routes as Ensembl data. Data can be accessed via:

• this web browser (go to http://bacteria.ensembl.org, http://metazoa.ensembl.org, etc., or to http://www.ensemblgenomes.org for the project homepage).
• through BioMarts (query optimised data warehouses) constructed for each of the Ensembl Genomes sites ( Bacteria Metazoa Protists Fungi Plants )
• via FTP (ftp.ensemblgenomes.org/pub)
• via the Ensembl Genomes public mysql server (mysql.ebi.ac.uk:4157:anonymous).
• using the Ensembl API.

The API has been modified slightly to support the existence of "genome collections", i.e. the existence of many small genomes in a single Ensembl database (a model which has been adopted for Ensembl Bacteria). The API makes the use of multi-genome databases transparent to users interested in a single genome, while methods to access a traditional, single-genome database,are unchanged. We aim to keep Ensembl Genomes software in synch with software releases of Ensembl, to ensure that users can access databases from across the taxonomic range using the same software.

See the documentation for more information about how to use Ensembl Genomes.

Featured content

The first release of Ensembl Plants contains 4 variation databases, including a new database built for Arabidopsis thaliana. The Arabidopsis variation database contains data from the screening of almost 400 strains using the Affymetrix 250k Arabidopsis SNP chip, and a new data set produced through a collaboration between Richard Mott at the Wellcome Trust Centre for Human Genetics in Oxford, Paula Kover at the University of Bath, and EBI, funded by the BBSRC. 17 lines of Arabdidopsis have been subjected to high throughput sequencing, leading to the identification of 2.9 million SNPs, the majority of which have not been previously reported. These can now be visualised in the Ensembl Plants browser: search for the gene of your choice, click on the "Gene" tab at the top of the page, and then select "Variation Image" or "Variation data" in the left hand menu. Click here to learn more about Ensembl variation databases.