FTP Download

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

Globus

For rapid bulk download of files, the Ensembl FTP site is available as an end point in the Globus Online system. In order to access the data you need to sign up for an account with Globus, install the Globus Connect Personal software and setup a personal endpoint to download the data. The Ensembl data is hosted at the EMBL-EBI end point called “Shared EMBL-EBI public endpoint”. Data from the Ensembl FTP site can then be found under the "/gridftp/ensemblorg/pub" directory within the EMBL-EBI public end point.

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 http://ftp.ebi.ac.uk/ensemblgenomes contains a README file, explaining the directory structure.

Multi-species data

DatabaseMySQLTSVEMFMAFXML
Pan_compara Multi-speciesMySQLTSVEMFXML
Protists 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)
YPlasmodium falciparum 3D7FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
YDictyostelium discoideumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
YPhytophthora infestansFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
YLeishmania majorFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Acanthamoeba castellanii str. Neff (GCA_000313135.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Achlya hypogyna str. ATCC 48635 (GCA_002081595.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Albugo laibachiiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Angomonas deanei (GCA_000442575.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aphanomyces astaci (GCA_002197585.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aphanomyces astaci (GCA_003546545.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aphanomyces astaci (GCA_003546565.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aphanomyces astaci (GCA_003546585.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aphanomyces astaci (GCA_003546605.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aphanomyces astaci (GCA_003546625.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aphanomyces astaci (GCA_003546765.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aphanomyces astaci (GCA_003546785.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aphanomyces astaci (GCA_003546805.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aphanomyces astaci (GCA_003546825.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aphanomyces astaci (GCA_003666305.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aphanomyces astaci str. APO3 (GCA_000520075.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aphanomyces invadans (GCA_003546525.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aphanomyces invadans str. NJM9701 (GCA_000520115.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Aureococcus anophagefferens (GCA_000186865.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Babesia bigemina str. Bond (GCA_000981445.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Babesia bovis str. T2Bo (GCA_000165395.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Babesia ovata str. Miyake (GCA_002897235.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Babesia sp. Xinjiang (GCA_002095265.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Besnoitia besnoiti str. Bb-Ger1 (GCA_002563875.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Bigelowiella natansFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Blastocystis hominis str. Singapore isolate B (sub-type 7) (GCA_000151665.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Capsaspora owczarzaki ATCC 30864 (GCA_000151315.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Cavenderia fasciculata str. SH3 (GCA_000203815.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Chroomonas mesostigmatica CCMP1168 (GCA_000286095.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Cryptomonas paramecium str. CCAP977/2A (GCA_000194455.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Cryptosporidium andersoni (GCA_001865355.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Cryptosporidium meleagridis str. UKMEL1 (GCA_001593445.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Cryptosporidium muris RN66 (GCA_000006515.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Cryptosporidium parvum Iowa II (GCA_000165345.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Cryptosporidium ubiquitum (GCA_001865345.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Cyclospora cayetanensis str. CHN_HEN01 (GCA_000769155.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Cystoisospora suis str. Wien I (GCA_002600585.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Dictyostelium purpureum str. QSDP1 (GCA_000190715.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Ectocarpus siliculosus str. Ec 32 (CCAP 1310/04) (GCA_000310025.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Eimeria acervulina (GCA_000499425.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Eimeria brunetti (GCA_000499725.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Eimeria maxima str. Weybridge (GCA_000499605.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Eimeria mitis (GCA_000499745.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Eimeria praecox (GCA_000499445.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Eimeria tenella str. Houghton (GCA_000499545.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Emiliania huxleyiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Entamoeba dispar SAW760 (GCA_000209125.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Entamoeba histolyticaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Entamoeba histolytica HM-1:IMSS-A (GCA_000365475.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Entamoeba histolytica HM-1:IMSS-B str. HM3:IMSS-B (GCA_000344925.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Entamoeba histolytica HM-3:IMSS (GCA_000346345.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Entamoeba histolytica KU27 (GCA_000338855.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Entamoeba histolytica str. HM1:IMSS clone 6 (GCA_001662325.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Entamoeba invadens IP1 (GCA_000330505.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Entamoeba nuttalli P19 (GCA_000257125.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Fonticula alba str. ATCC 38817 (GCA_000388065.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Fragilariopsis cylindrus CCMP1102 (GCA_001750085.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Giardia intestinalis ATCC 50581 str. GS/M H7 (GCA_000182405.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Giardia intestinalis assemblage B str. BAH15c1 (GCA_001543975.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Giardia intestinalis str. DH (GCA_000498715.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Giardia intestinalis str. GS (GCA_000498735.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Giardia lambliaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Giardia lamblia P15 (GCA_000182665.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Gregarina niphandrodes (GCA_000223845.4)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Guillardia theta CCMP2712FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Hammondia hammondi str. H.H.34 (GCA_000258005.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Hondaea fermentalgiana (GCA_002897355.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Hyaloperonospora arabidopsidisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Ichthyophthirius multifiliis str. G5 (GCA_000220395.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Kipferlia bialata (GCA_003568945.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Leishmania donovani str. BPK282A1 (GCA_000227135.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Leishmania infantum (GCA_900500625.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Leishmania panamensis str. MHOM/PA/94/PSC-1 (GCA_000755165.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Leptomonas pyrrhocoris str. H10 (GCA_001293395.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Leptomonas seymouri str. ATCC 30220 (GCA_001299535.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Monosiga brevicollis MX1 (GCA_000002865.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Naegleria gruberi str. NEG-M (GCA_000004985.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Nannochloropsis gaditana CCMP526 (GCA_000240725.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Nannochloropsis gaditana str. B-31 (GCA_000569095.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Nothophytophthora sp. Chile5 (GCA_001712635.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Oxytricha trifallax str. JRB310 (GCA_000295675.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Oxytricha trifallax str. JRB310 (GCA_000711775.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Paramecium tetraureliaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Perkinsela sp. CCAP 1560/4 (GCA_001235845.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Perkinsus marinus ATCC 50983 str. PmCV4CB5 2B3 D4 (GCA_000006405.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Peronospora effusa (GCA_003704535.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Peronospora effusa (GCA_003843895.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phaeodactylum tricornutumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQLGVFVCFVEP
Phytomonas sp. isolate EM1 (GCA_000582765.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytomonas sp. isolate Hart1 (GCA_000982615.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora cactorum str. 10300 (GCA_003287315.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora kernoviaeFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora kernoviae (GCA_001707905.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora kernoviae (GCA_001712645.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora kernoviae (GCA_001712705.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora kernoviae (GCA_001712715.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora lateralisFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora megakarya str. zdho120 (GCA_002215365.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora nicotianae (GCA_001482985.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora nicotianae (GCA_001483015.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora palmivora var. palmivora str. sbr112.9 (GCA_002911725.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora parasiticaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora parasitica CJ01A1 (GCA_000365545.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora parasitica INRA-310 (GCA_000247585.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora parasitica P10297 (GCA_000367145.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora parasitica P1976 (GCA_000365525.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora parasitica str. CHvinca01 (GCA_000509505.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora parasitica str. CJ02B3 (GCA_000509465.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora parasitica str. CJ05E6 (GCA_000509485.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora parasitica str. IAC_01/95 (GCA_000509525.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora ramorumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Phytophthora sojaeFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Planoprotostelium fungivorum str. Jena (GCA_003024175.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodiophora brassicae (GCA_001049375.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium bergheiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium berghei (GCA_900044335.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium berghei (GCA_900088445.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium berghei (GCA_900095585.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium berghei (GCA_900095635.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium chabaudiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium chabaudi adami (GCA_900095565.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium chabaudi chabaudi (GCA_900095605.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium coatneyi (GCA_001680005.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium cynomolgi strain B (GCA_000321355.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium falciparum 7G8 (GCA_000150435.3)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium falciparum CAMP/Malaysia (GCA_000521115.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium falciparum Dd2 (GCA_000149795.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium falciparum FCH/4 (GCA_000521155.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium falciparum HB3 (GCA_000149665.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium falciparum IGH-CR14 (GCA_000186055.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium falciparum MaliPS096_E11 (GCA_000521035.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium falciparum NF135/5.C10 (GCA_000521075.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium falciparum NF54 (GCA_000401695.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium falciparum NF54 (GCA_002831795.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium falciparum Palo Alto/Uganda (GCA_000521095.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium falciparum RAJ116 (GCA_000186025.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium falciparum Santa Lucia (GCA_000150455.3)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium falciparum Tanzania (2000708) (GCA_000521055.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium falciparum UGT5.1 (GCA_000401715.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium falciparum Vietnam Oak-Knoll (FVO) (GCA_000521015.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium fragile str. multiple (GCA_000956335.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium gaboni (GCA_001602025.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium gallinaceum (GCA_900005855.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium gonderi (GCA_002157705.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium inui San Antonio 1 (GCA_000524495.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium knowlesiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium knowlesi str. Malayan Strain Pk1 (A+) (GCA_002140095.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium knowlesi strain H (GCA_900004885.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium malariae (GCA_900088575.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium malariae (GCA_900090045.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium ovale (GCA_900090025.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium ovale curtisi (GCA_900088555.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium ovale curtisi (GCA_900088565.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium ovale wallikeri (GCA_900088485.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium ovale wallikeri (GCA_900088545.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium reichenowi (GCA_001601855.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium reichenowi (GCA_900097025.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium relictum (GCA_900005765.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium sp. DRC-Itaito (GCA_900240055.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium sp. DRC-Itaito (GCA_900257145.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium sp. gorilla clade G2 (GCA_900097015.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium vinckei petteri str. CR (GCA_000524515.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium vinckei vinckei (GCA_000709005.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium vivaxFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium vivax (GCA_900093555.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium vivax Brazil I (GCA_000320645.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium vivax India VII (GCA_000320625.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium vivax Mauritania I (GCA_000320665.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium vivax North Korean (GCA_000320685.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium yoelii 17X (GCA_000505035.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium yoelii str. 17X (GCA_900002385.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium yoelii str. YM (GCA_900002395.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmodium yoelii yoelii str. 17XNL (GCA_000003085.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Plasmopara halstedii (GCA_900000015.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Pseudo-nitzschia multistriataFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Pseudocohnilembus persalinus (GCA_001447515.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Pythium aphanidermatumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Pythium arrhenomanesFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Pythium irregulareFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Pythium iwayamaiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Pythium ultimumFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Pythium vexansFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Reticulomyxa filosa (GCA_000512085.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Salpingoeca rosetta str. ATCC 50818 (GCA_000188695.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Saprolegnia diclina VS20 (GCA_000281045.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Saprolegnia parasitica CBS 223.65 (GCA_000151545.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Sphaeroforma arctica JP610 (GCA_001186125.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Spironucleus salmonicida (GCA_000497125.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Stentor coeruleus (GCA_001970955.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Strigomonas culicis (GCA_000442495.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Stylonychia lemnae str. 130c (GCA_000751175.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Symbiodinium microadriaticum str. CCMP2467 (GCA_001939145.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Tetrahymena thermophilaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Thalassiosira oceanica str. CCMP1005 (GCA_000296195.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Thalassiosira pseudonanaFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Thecamonas trahens ATCC 50062 (GCA_000142905.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Theileria equi strain WA (GCA_000342415.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Theileria orientalis str. Fish Creek (GCA_003072545.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Theileria orientalis str. Goon Nure (GCA_003072535.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Theileria orientalis str. Robertson (GCA_003072525.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Theileria orientalis strain Shintoku (GCA_000740895.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Theileria parva str. Muguga (GCA_000165365.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Thraustotheca clavata str. ATCC 34112 (GCA_002081575.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Tieghemostelium lacteum str. TK (GCA_001606155.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Toxoplasma gondii ARI (GCA_000250965.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Toxoplasma gondii CAST (GCA_000256705.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Toxoplasma gondii COUG (GCA_000338675.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Toxoplasma gondii FOU (GCA_000224905.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Toxoplasma gondii GAB2-2007-GAL-DOM2 (GCA_000325525.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Toxoplasma gondii GT1 (GCA_000149715.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Toxoplasma gondii MAS (GCA_000224865.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Toxoplasma gondii ME49FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Toxoplasma gondii RUB (GCA_000224805.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Toxoplasma gondii TgCATBr9 (GCA_000224825.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Toxoplasma gondii TgCatPRC2 (GCA_000256725.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Toxoplasma gondii VAND (GCA_000224845.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Toxoplasma gondii VEG (GCA_000150015.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Toxoplasma gondii p89 (GCA_000224885.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Tritrichomonas foetus str. K (GCA_001839685.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trypanosoma bruceiFASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trypanosoma brucei equiperdum str. IVM-t1 (GCA_003543875.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trypanosoma conorhini (GCA_003719485.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trypanosoma cruzi (GCA_003719155.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trypanosoma cruzi (GCA_003719455.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trypanosoma cruzi Dm28c (GCA_000496795.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trypanosoma cruzi marinkellei (GCA_000300495.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trypanosoma cruzi str. CL Brener (GCA_000209065.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trypanosoma cruzi str. Dm28c (GCA_003177105.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trypanosoma cruzi str. TCC (GCA_003177095.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trypanosoma equiperdum (GCA_001457755.2)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trypanosoma rangeli (GCA_003719475.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trypanosoma rangeli SC58 (GCA_000492115.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF GFF3TSV RDF JSONMySQL--VEP
Trypanosoma theileri (GCA_002087225.1)FASTAFASTAFASTAFASTAFASTAEMBLGenBankGTF 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/protists/.

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.