Introduction

Ensembl 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 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.

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

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.

All data produced by the Ensembl project is freely available for your own use.