Custom data sets

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

FTP Download

API Code

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

Note: the API version needs to be the same as the databases you are accessing, so please use CVS 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 genomics	MySQL	EMF	BED	XML	Ancestral Alleles
BioMart	MySQL	-	-	-	-

Single species data

Species	DNA (FASTA)	cDNA (FASTA)	ncRNA (FASTA)	Protein sequence (FASTA)	Annotated sequence (EMBL)	Annotated sequence (GenBank)	Gene sets	Whole databases	Variation (EMF)	Variation (GVF)	Variation (VEP)	Regulation (GFF)	Data files	BAM
*Ailuropoda melanoleuca* (Panda)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Anolis carolinensis* (Anole lizard)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Bos taurus* (Cow)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	GVF	VEP	-	-	-
*Caenorhabditis elegans* (Caenorhabditis elegans)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Callithrix jacchus* (Marmoset)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Canis familiaris* (Dog)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	GVF	-	-	-	-
*Cavia porcellus* (Guinea Pig)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Choloepus hoffmanni* (Sloth)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Ciona intestinalis* (C.intestinalis)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Ciona savignyi* (C.savignyi)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Danio rerio* (Zebrafish)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	GVF	VEP	-	-	-
*Dasypus novemcinctus* (Armadillo)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Dipodomys ordii* (Kangaroo rat)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Drosophila melanogaster* (Fruitfly)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	GVF	-	-	-	-
*Echinops telfairi* (Lesser hedgehog tenrec)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Equus caballus* (Horse)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	GVF	-	-	-	-
*Erinaceus europaeus* (Hedgehog)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Felis catus* (Cat)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	GVF	-	-	-	-
*Gadus morhua* (Cod)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Gallus gallus* (Chicken)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	GVF	-	-	-	-
*Gasterosteus aculeatus* (Stickleback)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Gorilla gorilla* (Gorilla)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Homo sapiens* (Human)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	EMF	GVF	VEP	Regulation (GFF)	Regulation data files	-
*Latimeria chalumnae* (Coelacanth)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Loxodonta africana* (Elephant)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Macaca mulatta* (Macaque)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	GVF	-	-	-	-
*Macropus eugenii* (Wallaby)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Meleagris gallopavo* (Turkey)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Microcebus murinus* (Mouse Lemur)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Monodelphis domestica* (Opossum)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	GVF	-	-	-	-
*Mus musculus* (Mouse)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	EMF	GVF	VEP	Regulation (GFF)	Regulation data files	-
*Myotis lucifugus* (Microbat)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Nomascus leucogenys* (Gibbon)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Ochotona princeps* (Pika)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Oreochromis niloticus* (Tilapia)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	BAM
*Ornithorhynchus anatinus* (Platypus)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	GVF	-	-	-	-
*Oryctolagus cuniculus* (Rabbit)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Oryzias latipes* (Medaka)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Otolemur garnettii* (Bushbaby)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Pan troglodytes* (Chimpanzee)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	GVF	-	-	-	BAM
*Petromyzon marinus* (Lamprey)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Pongo abelii* (Orangutan)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	GVF	-	-	-	-
*Procavia capensis* (Hyrax)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Pteropus vampyrus* (Megabat)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Rattus norvegicus* (Rat)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	EMF	GVF	VEP	-	-	-
*Saccharomyces cerevisiae* (Saccharomyces cerevisiae)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	GVF	-	-	-	-
*Sarcophilus harrisii* (Tasmanian devil)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Sorex araneus* (Shrew)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Spermophilus tridecemlineatus* (Squirrel)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Sus scrofa* (Pig)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	GVF	-	-	-	BAM
*Taeniopygia guttata* (Zebra Finch)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	GVF	-	-	-	-
*Takifugu rubripes* (Fugu)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Tarsius syrichta* (Tarsier)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Tetraodon nigroviridis* (Tetraodon)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	GVF	-	-	-	-
*Tupaia belangeri* (Tree Shrew)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Tursiops truncatus* (Dolphin)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Vicugna pacos* (Alpaca)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-
*Xenopus tropicalis* (Xenopus)	FASTA	FASTA	FASTA	FASTA	EMBL	GenBank	GTF	MySQL	-	-	-	-	-	-

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.
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.

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 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 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.