FTP Download

Detailed information about the available data and file formats can be found here.

The data can also be downloaded directly from the Ensembl Plants FTP server.

Database dumps

Entire databases can be downloaded from our FTP site in a variety of formats. Please be aware that some of these files can run to many gigabytes of data.

Looking for MySQL dumps to install databases locally? Instructions for loading MySQL dumps onto a local MySQL server can be found on the Ensembl website.

Each directory on ftp.ensemblgenomes.org contains a README file, explaining the directory structure.

Programatic data access

Data can be accessed programatically in a number of ways, including the REST service and Perl API. For full details see the Programatic access documenation.

Multi-species data

Single species data

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

Metadata

Detailed metadata on the genomes provided by Ensembl Genomes is available from the FTP site in TSV, JSON and XML formats (format details).

Ensembl Plants: TSV | JSON | XML

Ensembl Genomes (all divisions): TSV | JSON | XML

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.).

The header line in an FASTA dump files containing DNA sequence consists of the following attributes : coord_system:version:name:start:end:strand This coordinate-system string is used in the Ensembl API to retrieve slices with the SliceAdaptor.

CDS

Coding sequences for Ensembl or ab initio predicted genes.

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 predictions.

Annotated sequence

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 any SQL database for a local installation of a mirror site. Generally, the FTP directory tree contains 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 mysql directory.

MAF (comparative data)

MAF files are provided for all pairwise alignments. The MAF file format is described here.

GVF (variation data)

GVF (Genome Variation Format) is a simple tab-delimited format derived from GFF3 for variation positions across the genome. There are GVF files for different types of variation data (e.g. somatic variants, structural variants etc). For more information see the "README" files in the GVF 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 columns are:

• chromosome name (may start with 'chr' for compliance with UCSC)
• start position. This is a 0-based position
• end position.

More information on the BED file format