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...
DAS: Ensembl now acts as a DAS (Distributed Annotation System) reference server. 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 servers

Ensembl maintains two public MySQL database servers, which you can access as user 'anonymous'.

ensembldb.ensembl.org

This server hosts the same Ensembl databases as www.ensembl.org. There are two options for retrieving data from this server:

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).
Important note: From release 48 you need a MySQL5-compatible client and to connect to port 5306; releases 47 and earlier are on MySQL4 and use the standard port (3306).

martdb.ensembl.org

Mart data is stored on a separate server. You can extract data using a MySQL client program; note that non-standard ports are used:

for releases up to and including version 47 (MySQL 4), use port 3316
for releases from version 48 onwards (MySQL 5), use port 5316

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.

Ensembl DAS

As well as acting as a DAS client to incorporate external data, Ensembl now acts as a DAS server, giving access to genomic sequences, the latest Ensembl gene predictions, and for some species, karyotypes and ditags. How to use Ensembl-DAS.

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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