Ensembl Genomes data is available through a number of routes - which you choose depends on the amount and type of data you wish to fetch.

Small quantities of data

Many of the pages displaying Ensembl Genomes genomic data offer an export option, suitable for small amounts of data, e.g. a single gene sequence.

Large datasets/complex analyses

If you require larger amounts of data (e.g. all the genes on a chromosome) or are conducting a more detailed analysis, we recommend using the Ensembl Perl API to access our publicly-accessible MySQL server. Ensembl Genomes also offers a language-independent REST service.

Alternatively, you can access a subset of Ensembl Genomes data using the DAS (Distributed Annotation System) protocol.

Complex cross-database queries

More complex datasets can be retrieved using the BioMart data-mining tool (not available for Ensembl Bacteria).

Whole datasets

If required, entire datasets can be downloaded from our FTP site in a variety of formats, from flat files to MySQL dumps.