FTP Download

You can download via a browser from our FTP site, use a script, or even use rsync from the command line.

API Code

If you do not have access to git, you can obtain our latest API code as a gzipped tarball:

Download complete API for this release

Note: the API version needs to be the same as the databases you are accessing, so please use git to obtain a previous version if querying older databases.

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? See our web installation instructions for full details.

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

Multi-species data

DatabaseMySQLTSVEMFMAFXML
Pan_compara Multi-speciesMySQLTSVEMFXML
Metazoa Multi-speciesMySQLTSVEMFMAFXML
Ensembl MartMySQL

Single species data

Popular species are listed first. You can customise this list via our home page.

SpeciesDNA (FASTA)cDNA (FASTA)CDS (FASTA)ncRNA (FASTA)Protein sequence (FASTA)Annotated sequence (EMBL)Annotated sequence (GenBank)Gene setsOther annotationsWhole databasesVariation (GVF)Variation (VCF)Variation (VEP)
YCaenorhabditis elegansFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
YAnopheles gambiaeFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
YDrosophila melanogasterFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
YApis mellifera (DH4)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
YBombyx moriFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
YOctopus bimaculoidesFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Actinia equina (AE1) - GCA_011057435.1FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Acyrthosiphon pisumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Adineta vagaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aedes aegypti (LVP_AGWG)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Aedes albopictusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Amphimedon queenslandicaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles albimanusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles arabiensisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles atroparvusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles christyiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles coluzziiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles coluzzii (Ngousso)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles culicifaciesFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles darlingiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles dirusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles epiroticusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles farautiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles funestusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles maculatusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles melasFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles merusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles minimusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles quadriannulatusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles sinensisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles sinensis (China)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Anopheles stephensiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anopheles stephensi (Indian)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Anoplophora glabripennisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Atta cephalotesFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Belgica antarcticaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bemisia tabaci (ASIAII-5)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bemisia tabaci (SSA1-SG1 NG)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bemisia tabaci (SSA1-SG1 UG)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bemisia tabaci (SSA2 NG)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bemisia tabaci (SSA3 NG)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bemisia tabaci (Sweetpotato Uganda)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Biomphalaria glabrataFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Bombus impatiensFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bombus terrestrisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Branchiostoma lanceolatumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Brugia malayiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Caenorhabditis brenneriFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Caenorhabditis briggsaeFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Caenorhabditis japonicaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Caenorhabditis remaneiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Capitella teletaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Cimex lectulariusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Clytia hemisphaerica (Z4C2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Crassostrea gigasFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Culex quinquefasciatusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Culicoides sonorensisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Danaus plexippusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Daphnia magnaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Daphnia pulexFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Dendroctonus ponderosaeFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Dinothrombium tinctoriumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila ananassae (TSC#14024-0371.13)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila erecta (TSC#14021-0224.01)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila grimshawi (TSC#15287-2541.00)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila mojavensis (TSC#15081-1352.22)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila persimilis (MSH-3)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila pseudoobscura pseudoobscura (MV2-25)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila sechellia (Rob3c)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila simulans (w501)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila virilis (TSC#15010-1051.87)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila willistoni (TSC#14030-0811.24)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Drosophila yakuba (Tai18E2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Folsomia candida str. VU populationFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Glossina austeniFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Glossina brevipalpisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Glossina fuscipes fuscipesFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Glossina morsitansFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Glossina pallidipesFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Glossina palpalisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Heliconius melpomeneFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Helobdella robustaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Hofstenia miamiaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Ixodes scapularisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Ixodes scapularis (ISE6)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Lepeophtheirus salmonisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Leptotrombidium delienseFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Lingula anatinaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Loa loaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Lottia giganteaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Lucilia cuprinaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Lutzomyia longipalpisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Mayetiola destructorFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Megaselia scalarisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Melitaea cinxiaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Mnemiopsis leidyiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Musca domesticaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Nasonia vitripennis (AsymCx)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Nematostella vectensisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Onchocerca volvulusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Orchesella cinctaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Pediculus humanusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phlebotomus papatasiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Pristionchus pacificusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Rhodnius prolixusFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Sarcoptes scabieiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Schistosoma mansoniFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Solenopsis invictaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Stegodyphus mimosarumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Stomoxys calcitransFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Strigamia maritimaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Strongylocentrotus purpuratus (Spur 01)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Strongyloides rattiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Teleopsis dalmanniFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Tetranychus urticaeFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Thelohanellus kitaueiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Tigriopus californicus (San Diego)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trialeurodes vaporariorum (IVF)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Tribolium castaneumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trichinella spiralisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trichoplax adhaerensFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Varroa destructorFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Zootermopsis nevadensisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP

Metadata

Data files containing metadata for Ensembl Genomes from release 15 onwards can be found in the root directory or appropriate division directory of each release e.g. /current/metazoa/.

The following files are provided:

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

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.
GFF3
GFF3 provides access to all annotated transcripts which make up an Ensembl gene set. This file format is described here.
EMF flatfile dumps (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 containing human (GRCh38), and all multiple 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.
VCF (variation data)
VCF (Variant Call Format) is a text file format containing meta-information lines, a header line, and then data lines each containing information about a position in the genome. This file format can also contain genotype information on samples for each position. More details about the format and its specifications are available here.
VEP (variation data)
Compressed text files (called "cache files") used by the Variant Effect Predictor tool. More information about these files is available here.
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...

Tarball

The entire Ensembl API is gzipped and concatenated into a single TAR file. This is updated daily.