Accessing Ensembl Data

Ensembl data is available through a number of routes - which you choose depends on the amount and type of data you wish to fetch. Please note that Ensembl coordinates always have a one-based start.

Small quantities of data

Many of the pages displaying Ensembl 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 our publicly-accessible MySQL server. We provide a Perl API to these databases, so they can be scripted against without needing to know the database schema.

If you are not familiar with Perl, we recommend using our REST server. Various REST endpoints provide access to vast amounts of Ensembl data.

Complex cross-database queries

More complex datasets can be retrieved using the BioMart data-mining tool.

Whole databases

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