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Custom data sets

If you want to filter or customise your download, please try Biomart, a web-based querying tool.

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.ensembl.org contains a README file, explaining the directory structure.

Multi-species data

Database
Comparative genomicsMySQLEMFBEDXMLAncestral Alleles
BioMartMySQL----
Stable idsMySQL----

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 setsWhole databasesVariation (GVF)Variation (VCF)Variation (VEP)Regulation (GFF)Data filesBAM
YHuman
Homo sapiens
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEPRegulation (GFF)Regulation data filesBAM
YMouse
Mus musculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEPRegulation (GFF)Regulation data filesBAM
YZebrafish
Danio rerio
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP--BAM
Alpaca
Vicugna pacos
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Anole lizard
Anolis carolinensis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP--BAM
Armadillo
Dasypus novemcinctus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP--BAM
Bushbaby
Otolemur garnettii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
C.intestinalis
Ciona intestinalis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
C.savignyi
Ciona savignyi
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Caenorhabditis elegans
Caenorhabditis elegans
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Cat
Felis catus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP--BAM
Cave fish
Astyanax mexicanus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP--BAM
Chicken
Gallus gallus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP--BAM
Chimpanzee
Pan troglodytes
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP--BAM
Chinese softshell turtle
Pelodiscus sinensis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP--BAM
Cod
Gadus morhua
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Coelacanth
Latimeria chalumnae
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Cow
Bos taurus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP---
Dog
Canis lupus familiaris
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP--BAM
Dolphin
Tursiops truncatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Duck
Anas platyrhynchos
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Elephant
Loxodonta africana
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Ferret
Mustela putorius furo
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP--BAM
Flycatcher
Ficedula albicollis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP--BAM
Fruitfly
Drosophila melanogaster
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP---
Fugu
Takifugu rubripes
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Gibbon
Nomascus leucogenys
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP---
Gorilla
Gorilla gorilla gorilla
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Guinea Pig
Cavia porcellus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Hedgehog
Erinaceus europaeus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Horse
Equus caballus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP---
Hyrax
Procavia capensis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Kangaroo rat
Dipodomys ordii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Lamprey
Petromyzon marinus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Lesser hedgehog tenrec
Echinops telfairi
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Macaque
Macaca mulatta
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP---
Marmoset
Callithrix jacchus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Medaka
Oryzias latipes
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Megabat
Pteropus vampyrus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Microbat
Myotis lucifugus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Mouse Lemur
Microcebus murinus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Opossum
Monodelphis domestica
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP--BAM
Orangutan
Pongo abelii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP--BAM
Panda
Ailuropoda melanoleuca
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Pig
Sus scrofa
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP--BAM
Pika
Ochotona princeps
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Platyfish
Xiphophorus maculatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP--BAM
Platypus
Ornithorhynchus anatinus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP--BAM
Rabbit
Oryctolagus cuniculus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP--BAM
Rat
Rattus norvegicus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP---
Saccharomyces cerevisiae
Saccharomyces cerevisiae
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP---
Sheep
Ovis aries
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP--BAM
Shrew
Sorex araneus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Sloth
Choloepus hoffmanni
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Spotted gar
Lepisosteus oculatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP--BAM
Squirrel
Ictidomys tridecemlineatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Stickleback
Gasterosteus aculeatus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Tarsier
Tarsius syrichta
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Tasmanian devil
Sarcophilus harrisii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP--BAM
Tetraodon
Tetraodon nigroviridis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP---
Tilapia
Oreochromis niloticus
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP--BAM
Tree Shrew
Tupaia belangeri
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Turkey
Meleagris gallopavo
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP---
Wallaby
Macropus eugenii
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Xenopus
Xenopus tropicalis
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQL--VEP---
Zebra Finch
Taeniopygia guttata
FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTFMySQLGVFVCFVEP---

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.
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.

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...

Tarball

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