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What's New in Release 46

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To access Ensembl Genomes data from any programming language, try our REST service. For full documentation including examples from a wide range of languages, visit http://rest.ensemblgenomes.org

Release 46 of Ensembl Bacteria has an updated pan-taxonomic compara (which includes key bacterial species) and a fresh set of flat files on the FTP server. There are no other significant changes from the last release to the genomes and genes. There are a total of 44,048 genomes.

Archive sites

Archive of release 45 of EnsemblBacteria: eg45-bacteria.ensembl.org (Sep 2019)

Archive of release 40 of EnsemblBacteria: eg40-bacteria.ensembl.org (July 2018)

Archive of release 37 of EnsemblBacteria: eg37-bacteria.ensembl.org (October 2017)

Ensembl Bacteria

Ensembl Bacteria is a browser for bacterial and archaeal genomes. These are taken from the databases of the International Nucleotide Sequence Database Collaboration(the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Database of Japan).

Non-redundant genomes

As of release 35 (April 2017), we have only integrated new sequences that are non-redundant when compared to the existing data set, according to the criteria of the UniProt Knowledgebase (DOI: 10.1093/database/baw139). From early 2020, we will only be hosting non-redundant prokarotic genomes. All existing data will be continue to be available via the archive sites.

Data access

Data can be visualised through the Ensembl genome browser and accessed programmatically via our Perl and RESTful APIs. Data is also accessible through public MySQL databases and our FTP site containing full data dumps in FASTA, EMBL, GTF, GFF3, JSON and RDF formats. A selection of over 100 key bacterial genomes have been included in the pan-taxonomic compara, and genes from all genomes have been classified into families using HAMAP and PANTHER (more details).

Ensembl Genomes is developed by EMBL-EBI and is powered by the Ensembl software system for the analysis and visualisation of genomic data. For details of our funding please click here.

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