Ensembl .All data sets generated by the Ensembl project are freely available to download from the ftp.ensembl.org site. Please see also the disclaimer.
Please note: 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.
Additionally, Ensembl would like to encourage users to directly extract information from our databases via SQL rather than downloading huge flat files. We offer a public MySQL interface at ensembldb.ensembl.org (and martdb.ensembl.org:3316) that accepts SQL queries as user 'anonymous'. Client programs for accessing this interface are available via MySQL.
It is also possible to install the Ensembl API code locally and configure it to access databases on ensembldb.ensembl.org and martdb.ensembl.org. Users can develop their own analysis scripts to access Ensembl's object orientated representation of biological objects. This is much easier than querying SQL and avoids downloading huge databases.
Ensembl provides sequence databases of gene, transcript and protein predictions. These sequences are suitable for a local installation of a sequence similarity search system. MySQL database table dumps are available for all databases underlying the Ensembl system. These text format dumps can be imported into relational database management systems which would enable installation of a complete Ensembl mirror site.
There are three types of data dumps for each species on the FTP site:
FASTA - FASTA sequence databases of Ensembl gene, transcript and protein model predictions. Since the FASTA format does not permit sequence annotation, these database files are mainly intended for use with local sequence similarity search algorithms. Please see the FASTA files document for a more detailed description of the header line format and the file naming conventions.
DNA - Masked and unmasked genome sequences associated with the assembly (contigs, chromosomes etc.).
cDNA - cDNA sequences for Ensembl or ab initio predicted genes.
Peptides - Protein sequences for Ensembl or ab initio predicted genes.
RNA - Non-coding RNA gene preditions.
Flatfile - Flat files allow more extensive sequence annotation by means of feature tables and contain thus the genome sequence as annotated by the automated Ensembl genome annotation pipeline. Each nucleotide sequence record in a flat file represents a 1Mb slice of the genome sequence. Flat files are broken into chunks of 1000 sequence records for easier downloading.
EMBL - Ensembl database dumps in EMBL nucleotide sequence database format
GenBank - Ensembl database dumps in GenBank nucleotide sequence database format
MySQL - Database table dumps in text format, as well as SQL table definition files should be portable to any SQL database. Generally, the FTP directory tree contains one one directory per database. For more information about these databases and their associated Application Programming Interfaces (or APIs) see the software section.
These additional documents explain the FTP directory structure and the FASTA file naming and header conventions used on this site.
© 2009 WTSI / EBI. Ensembl is available to download for public use - please see the code licence for details.
