The Ensembl Genomes 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.
The data for this release is available at /current. The data from previous releases are available at .
To facilitate storage and download all databases are GNU Zip (gzip, *.gz) compressed.
Please note: Ensembl Genomes 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.
| Species | Files | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Schizosaccharomyces pombe (Schizosaccharomyces pombe) | FASTA (DNA) | FASTA (cDNA) | FASTA (protein) | EMBL | GenBank | MySQL | GTF | - | - | - | - |
| Pan_compara Multi-species | - | - | - | - | - | mySQL | - | EMF | - | - | TSV |
| Fungal Multi-species | - | - | - | - | - | mySQL | - | EMF | - | - | TSV |
| Ensembl Mart | - | - | - | - | - | mySQL | - | - | - | - | - |
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 protein-coding genes
- Peptides
- Protein sequences for protein-coding genes.
- RNA
- Non-coding RNA gene preditions.
- Flatfile
- Flat files allow more extensive sequence annotation by means of feature tables. The currently annotation displayed in Ensembl Genomes consists of protein calling genes derived from one of the following data resources:
- EMBL Nucleotide Sequence Database (used for Ensembl Bacteria)
- VectorBase (used for insect vectors of human diseases)
- WormBase (used for Caenorhaditis elegans)
- FlyBase (used for Drosophila melanogaster)
- PlasmoDB (used for Plasmodium falciparum
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 Genomes database dumps in EMBL nucleotide sequence database format
- GenBank
- Ensembl Genomes database dumps in GenBank nucleotide sequence database format
- MySQL
- All Ensembl Genomes 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 (where available) 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 compara directory.
Note: the EMF directories for compara also contain trees in phyloxml, nh and newick format.
- TSV
- Tab separated files containing selected data for individual species and from comparative genomics provided for convenience. All files are gzipped and contain header lines detailing the contents of each file. The files available are: Per species: <species_name>.<assembly>.<release>.uniprot.tsv - Provides mappings from Gene, Transcript and Translation stable identifiers to UniProtKB accessions with reports as to the % identity of the hit where applicable. Per compara: Compara.homologies.<release>.tsv - Homologies and identity between proteins in different species retrieved from Compara. Compara.stableid_to_genetreeid.<release>.tsv - Provides mappings from compara gene tree stable identifiers to the component gene and translation stable identifiers.
Each directory on ftp.ensemblengenomes.org contains a README file. This additional document explains the FTP directory structure.
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 Genomes (all divisions): TSV | JSON | XML