The Ensembl FTP Server

If required, entire databases can be downloaded from our FTP site in a variety of formats, from flat files to MySQL dumps. Please be aware that these files can run to many gigabytes of data.

To facilitate storage and download all databases are GNU Zip (gzip, *.gz) compressed.

Please note: Ensembl supports downloading of many 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 database dumps.

About the data

The following types of data dumps are available 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. Each directory has a README file with a 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

All Ensembl MySQL databases are available in text format as are the SQL table definition files. These can be imported into to any SQL database for a local installation of a mirror site. Generally, the FTP directory tree contains one one directory per database. For more information about these databases and their Application Programming Interfaces (or APIs) see the API section.

GTF

Gene sets for each species. These files include annotations of both coding and non-coding genes. This file format is described here.

EMF flatfile dumps (variation and comparative data)

Alignments of resequencing data are available for several species as Ensembl Multi Format (EMF) flatfile dumps. The accompanying README file describes the file format.

Also, the same format is used to dump whole-genome multiple alignments as well as gene-based multiple alignments and phylogentic trees used to infer Ensembl orthologues and paralogues. These files are available in the ensembl_compara database which will be found in the multi_species directory.

BED format files (comparative data)

Constrained elements calculated using GERP are available in BED format. For more information see the accompanying README file.

BED format is a simple line-based format. The first 3 mandatory column are:

• chromosome name, starting with chr to be compiant with UCSC browser. Example: chrX
• start position. This is a 0-based position
• end position.

More information on the BED file format is available here.

Each directory on ftp.ensembl.org contains a README file. This additional document explains the FTP directory structure.