The following types of data dumps are available on the FTP site. To facilitate storage and download all databases are GNU Zip (gzip, *.gz) compressed.
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 Ensembl or ab initio predicted genes.
Peptides - Protein sequences for Ensembl or ab initio predicted genes.
RNA - Non-coding RNA gene preditions.
Flatfile - 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 - 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 multi_species directory.
Each directory on ftp.ensembl.org contains a README file. This additional document explains the FTP directory structure.
| Species | DNA | cDNA | Peptides | EMBL | GenBank | MySQL | GTF | EMF | GFF |
|---|---|---|---|---|---|---|---|---|---|
| Aedes aegypti (yellow fever mosquito) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Anopheles gambiae (African malaria mosquito) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Bos taurus (cattle) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Caenorhabditis elegans (nematode) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Canis familiaris (dog) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Cavia porcellus (domestic guinea pig) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Ciona intestinalis (Sea squirt Ciona intestinalis) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Ciona savignyi (Sea squirt Ciona savignyi) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Danio rerio (zebrafish) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Dasypus novemcinctus (nine-banded armadillo) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Drosophila melanogaster (fruit fly) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Echinops telfairi (small Madagascar hedgehog) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Equus caballus (horse) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Erinaceus europaeus (western European hedgehog) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Felis catus (cat) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Gallus gallus (chicken) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Gasterosteus aculeatus (three spined stickleback) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Homo sapiens (human) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | FTP | FTP |
| Loxodonta africana (African savanna elephant) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Macaca mulatta (rhesus monkey) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Microcebus murinus (grey mouse lemur) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Monodelphis domestica (gray short-tailed opossum) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Mus musculus (house mouse) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - |
| Myotis lucifugus (little brown bat) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Ochotona princeps (American pika) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Ornithorhynchus anatinus (platypus) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Oryctolagus cuniculus (rabbit) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Oryzias latipes (Japanese medaka) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Otolemur garnettii (small-eared galago) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Pan troglodytes (chimpanzee) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Pongo pygmaeus (orangutan) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Rattus norvegicus (Norway rat) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - |
| Saccharomyces cerevisiae (baker's yeast) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Sorex araneus (European shrew) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Spermophilus tridecemlineatus (thirteen-lined ground squirrel) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Takifugu rubripes (torafugu) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Tetraodon nigroviridis (Fresh water pufferfish) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Tupaia belangeri (northern tree shrew) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Xenopus tropicalis (western clawed frog) | FTP | FTP | FTP | FTP | FTP | FTP | FTP | - | - |
| Multi-species | - | - | - | - | - | FTP | - | FTP | |
| Ensembl Mart | - | - | - | - | - | FTP | - | - |
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