Ensembl .

Information Data Downloads

Ensembl data is available through a number of routes:

Export from Ensembl web pages

Many of the pages displaying Ensembl genomic data offer an export option, suitable for small amounts of data. More...

Public MySQL server

For larger amounts of data and more detailed analysis, we recommend you use our publicly-accessible MySQL server. More...

FTP

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

BioMart

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

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

Exporting from Ensembl pages

This is the ideal option if you want a short sequence as a FASTA file, or a GFF file of a few features in a region. Simply find your desired feature or region, click on one of the "Export..." links in the left-hand menu, and select your output options.

We respectfully request that users do not script against the export pages on the Ensembl website, as this degrades the service for other web servers. The public MySQL server (see below) is provided specifically for this purpose. Thank you.

Public MySQL server

Ensembl maintains a public MySQL database server, ensembldb.ensembl.org, which you can access as user 'anonymous'.

There are two options for retrieving data from this database:

Perl API

The easiest option is to use the Ensembl Perl API. The API uses an object-oriented approach to model real biological objects such as genes, transcripts and 'slices' of DNA sequence, making it straightforward for you to write scripts that retrieve and analyze data.

MySQL client

Alternatively, you can use a MySQL client program to query the database directly. However this does require knowledge of the complex database schemas used by Ensembl, so we only recommend it if you are unable to install our API (e.g. if you have no access to Perl).

FTP

All of the data used on the main Ensembl website can be downloaded from our public FTP server. Please be aware that these files can run to many gigabytes of data.

For a list of which databases are needed for an Ensembl mirror site, please see the website installation instructions.

BioMart

Ensembl supports downloading of many more correlation tables via the highly customisable BioMart data mining tool. You may find exploring this web-based data mining tool easier than extracting information from our normalised database dumps.

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© 2008 WTSI / EBI. Ensembl is available to download for public use - please see the code licence for details.