Ensembl Genomes Home
Bacteria | Protists | Fungi | Plants | Metazoa | Vertebrates

About

The Ensembl genome annotation system, developed jointly by the EBI and the Wellcome Trust Sanger Institute, has been used for the annotation, analysis and display of vertebrate genomes since 2000. Since 2009, the Ensembl site has been complemented by the creation of five new sites, for bacteria, protists, fungi, plants and invertebrate metazoa, enabling users to use a single collection of (interactive and programatic) interfaces for accessing and comparing genome-scale data from species of scientific interest from across the taxonomy.

aedesMetazoa
 
plasmodiumProtists
 
bacillusBacteria
 
pombe
pombe
e!-thumb or browse vertebrate
genomes in Ensembl
In each domain, we aim to bring the integrative power of Ensembl tools for comparative analysis, data mining and visualisation across genomes of scientific interest, working in collaboration with scientific communities to improve and deepen genome annotation and interpretation.

Releases

What's New in Release 12 (December 2011)

The twelfth release of Ensembl Genomes features updates to version 65 of the Ensembl software across all divisions, and a number of new genomes bringing the total number of genomes to 335 (full list). Detailed notes can be found here. See the individual homepages for Bacteria, Protists, Fungi, Plants and Metazoa for more information.

Ensembl Bacteria
Ensembl Bacteria now includes operon data from RegulonDB for E. coli K12.
Ensembl Protists
No significant data updates have been made to the portal for Ensembl Protists.
Ensembl Fungi
The latest release of Ensembl Fungi now includes Ashbya gossypii. The annotation for S. pombe has been updated to reflect the most recent content from PomBase.
Ensembl Plants
Ensembl Plants now includes the genome of the red alga Cyanidioschyzon merolae, and has had significant updates to the gene models of the bryophyte Physcomitrella patens and the soybean Glycine max.
Ensembl Metazoa
The 12th release of Ensembl Metazoa includes the three new genomes of Atta cephalotes, a leaf-cutting ant, Tribolium castaneum, the red flour beetle, and Bombyx mori, a domesticated silkmoth.

Future Releases

Release 13 of Ensembl Genomes is scheduled for 6th March 2012. Detailed notes for this can be found here.

Release notes from previous releases

Working with communities

Ensembl Genomes aims to work with all sections of the scientific community to represent the best annotation for every genome. Our role varies according to the species, and while it may include genome assembly, gene prediction and functional annotation, we are also committed to providing a portal through which genomic data from model organism and community databases can be visualised and analysed in their wider context, and integrated with other data stored in the core repositories maintained by the EBI. The current release of Ensembl Genomes includes databases developed by (or in partnership with) the groups shown on the right:

Collaborate with us

Ensembl Genomes is always looking to engage with new communities. We are highly interested in collaborations that develop resources for genomes in particular areas of interest, and we have a growing range of tools to assist groups with genome sequence to build Ensembl databases and incorporate their data in Ensembl Genomes. If you have data you would like to bring into Ensembl Genomes, mail our helpdesk and we'll be happy to advise you on possible approaches.
CADRE
Gramene
VectorBase
WormBase
PomBase

Featured content

Do you have genome-centric data you would like to see in Ensembl Genomes? Did you know that polymorphisms, sequence alignments and other data can be imported for visualisation alongside the reference genomic sequence and annotation? There are a number of ways this can be achieved: for example, you can upload your data into a private area on our database servers, or set up a DAS server if you want to allow others to see your data in the site. But recently, new functionality has been developed to allow the visualisation of data directly from your local files via HTTP or FTP. Files supported include most popular formats, including BAM, VCF and GFF, along with wiggle tracks.
See our help pages for more information. This month, Ensembl Genomes are now partners in a new site providing access to genomic data from the model organism Schizosaccharomyces pombe. PomBase is funded by the Wellcome Trust and integrates genomic annotation of the sequence (provided using Ensembl technology) with deep manual curation of the scientific literature. The latest content produced through PomBase will be reflected in each subsequent release of Ensembl Fungi, alongside data from other fungal species.
Ensembl Genomes is a project run by EMBL - EBI to maintain annotation on selected genomes, based on the software developed in the Ensembl project developed jointly by the EBI and the Wellcome Trust Sanger Institute Sanger