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Access to over 20,000 Bacterial Genomes
What's New in Release 27
Release 27 of Ensembl Bacteria has been loaded from EMBL-Bank release 123 into 96 multispecies Ensembl v80 databases. The current dataset contains 23,000 genomes (22,703 bacteria and 297 archaea) containing 81,857,152 protein coding genes loaded from 2,047,782 INSDC entries.This release includes 1239 new genomes, 52 genomes with updated assemblies, 888 genomes with updated annotation, 86 genomes where the assigned name has changed, and 6 genomes removed since the last release. Operon and related data from RegulonDB has been loaded for E. coli K12 MG1655.
Release 28 of Ensembl Genomes is scheduled for 28th July 2015 - more details in Ensembl Genomes Release 28 Intentions. Note that this release is principally concerned with updating to a newer version of the Ensembl platform and contains relatively little additional data.
Over 20,000 genome sequences from bacteria and archaea 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 genomes from bacteria and archaea (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)
Ensembl Bacteria has been developed with the support of the Microme project, a resource for bacterial metabolism.