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. 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.

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.