Ensembl Bacteria
Over 6000 bacterial genome sequences have been annotated and deposited in the public archives of the members of the International Nucleotide Sequence Database Collaboration. This site provides access to complete, annotated bacterial genomes (present in the European Nucleotide Archive) through the Ensembl graphical user interface (genome browser). More details about the integration are provided here
Programmatic access is available through the Ensembl Perl and REST-ful APIs and through publicly accessible mysql databases, along with full data dumps (including DNA sequence and protein sequence in FASTA format, annotations in GTF format, and mysql dump files). Due to the large number of these databases, there is some modification to the APIs, and database and FTP site structure, compared to that used for other branches of the taxonomy (e.g. the storage of many genomes in one database; the provision of lookup services to identify genomes by INSDC identifiers, taxonomy identifiers, or partial names. Full details are available here.
BioMart access is not available, but we are working on providing new, more powerful data mining tools to allow users to exploit these genomes. A selection of over 100 key bacterial genomes has been included in the pan-taxonomic Compara, and genes from all genomes are classified into families using HAMAP and PANTHER (more details)
Strigamia maritima and Megaselia scalaris genomes 
In Release 18 we have added Strigamia maritima, a coastal European centipede, and Megaselia scalaris, a scuttle fly of the Phoridae family, also known as the coffin fly or humpbacked fly.
Brugia malayi genome
A new version of the nematode Brugia malayi genome, a causative agent of lymphatic filariasis, has been assembled and annotated in a collaboration between WormBase, the University of Pittsburgh, and the Brugia malayi community. Further details...
Barley synteny
Whole genome alignments between barley, rice, and brachypodium allow the syntenic relationships between these species to be explored. See barley chromosome 2 vs. rice or barley chromosome 2 vs. brachypodium.
Wheat sequence search
We have developed a new sequence search facility for the available wheat genome sequence data. Alignments between your sequences and wheat are returned in the genomic context of brachypodium. Search here...
GO annotation extensions
Annotation with Gene Ontology terms can now use annotation extensions to provide a richer and more detailed level of annotation (currently available for Schizosaccharomyces pombe). View example...
Releases
Have a question?
New 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 you would like to see, contact us.
What's New in Release 18 (April 2013)
The eighteenth release of Ensembl Genomes features updates to version 71 of the Ensembl software across all divisions, and a number of new genomes (including 6,305 genomes in the latest version of Ensembl Bacteria) bringing the total number of genomes to 6431 (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 has been updated and now includes 6,305 bacterial genomes deposited in the European Nucleotide Archive.
Ensembl Fungi
New genomes have been added for the industrially important fungi Yarrowia lipolytica and Trichoderma reesei, and the opportunistic pathogen Cryptococcus neoformans, and a new assembly added for Botryotinia fuckeliana. The annotation for Schizosaccharomyces pombe has also been updated to the latest version available from PomBase.
Ensembl Metazoa
Four new species have been added: two parasitic nematodes, Brugia malayi and Loa loa, which are causative agents of lymphatic and subcutaneous filariasis, respectively; Megaselia scalaris, a scuttle fly; and the centipede Strigamia maritima, the first myriapod genome. Two other species have updated genome assemblies: the nematode Caenorhabditis elegans; and Schistosoma mansoni, a blood-fluke and a major agent of schistosomiasis.
Ensembl Plants
This release adds a second legume, Medicago truncatula (barrel clover), visualisation of the Hordeum vulgare (barley) physical map anchoring the gene-ome, and whole genome alignmetns between barley, rice and brachypodium. Updates include migrating Zea mays (maize) to assembly version 3, enabling the assembly converter tool between these versions, and new variation datasets for barley and Brachypodium distachyon as well as alignments of Triticum aestivum (bread wheat) WGS, TSA and EST assemblies against these cereal genomes. In addition we have updated our protein domain predictions and cross references for almost all genomes, and created new pairwise alignments between several genome sequences. Read more on the Ensembl Plants homepage for details.
Ensembl Protists
This release extends the taxonomy coverage of Ensembl Protists with the addition of Cryptophyte genome, Guillardia theta. The DNA alignments and synteny is also updated for the stramenopiles genomes.
Future Releases
Release 19 of Ensembl Genomes is scheduled for 2nd July 2013. Detailed notes for this can be found here.
Release notes from previous releases
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.
