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Access to over 20,000 Bacterial Genomes
What's New in Release 30
Release 30 of Ensembl Bacteria has been loaded from EMBL-Bank release 124 into 124 multispecies Ensembl v83 databases. The current dataset contains 29,777 genomes (29,395 bacteria and 382 archaea) containing 103,544,533 protein coding genes loaded from 2,713,864 INSDC entries. Annotation from PHIbase 4.0 has been included for 1163 genes from 181 genomes (example)
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.