Custom data sets

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

FTP Download

Detailed information about the available data and file formats can be found here.

The data can also be downloaded directly from the Ensembl Protists FTP server.

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? Instructions for loading MySQL dumps onto a local MySQL server can be found on the Ensembl website.

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

Programatic data access

Data can be accessed programatically in a number of ways, including the REST service and Perl API. For full details see the Programatic access documenation.

Multi-species data

DatabaseMySQLTSVEMFMAF
Pan_compara Multi-speciesMySQLTSVEMF
Protists Multi-speciesMySQLTSVEMFMAF
Ensembl MartMySQL

Single species data

SpeciesDNAcDNACDSncRNAProteinEMBLGENBANKMySQLTSVGTFGFF3GVFVCFVEP
Acanthamoeba castellanii_str_neffFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Albugo candidaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Albugo laibachiiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Angomonas deaneiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Aphanomyces astaciFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Aphanomyces invadansFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Aureococcus anophagefferensFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Babesia bigeminaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Babesia bovisFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Babesia microti_strain_riFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Bigelowiella natansFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Bigelowiella natans_gca_000002455FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Blastocystis hominisFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Bodo saltansFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Capsaspora owczarzaki_atcc_30864FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Chroomonas mesostigmatica_ccmp1168FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Cryptomonas parameciumFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Cryptosporidium muris_rn66FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Cryptosporidium parvumFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Cryptosporidium parvum_iowa_iiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Dictyostelium discoideumFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(otherfeatures)
MySQL(funcgen)
TSVGTFGFF3VEP
Dictyostelium fasciculatumFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Dictyostelium lacteumFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Dictyostelium purpureumFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Eimeria acervulinaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Eimeria brunettiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Eimeria maximaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Eimeria mitisFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Eimeria necatrixFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Eimeria praecoxFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Eimeria tenellaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Eimeria tenella_gca_000499545FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Emiliania huxleyiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Entamoeba dispar_saw760FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Entamoeba histolyticaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Entamoeba histolytica_hm_1_imss_aFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Entamoeba histolytica_hm_1_imss_bFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Entamoeba histolytica_hm_3_imssFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Entamoeba histolytica_ku27FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Entamoeba invadens_ip1FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Entamoeba nuttalli_p19FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Fonticula albaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Giardia intestinalisFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Giardia intestinalis_assemblage_bFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Giardia intestinalis_atcc_50581FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Giardia intestinalis_gca_000498715FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Giardia lambliaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Giardia lamblia_p15FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Gregarina niphandrodesFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Guillardia thetaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Hammondia hammondiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Hyaloperonospora arabidopsidisFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Ichthyophthirius multifiliisFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Leishmania braziliensis_mhom_br_75_m2904FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Leishmania donovani_bpk282a1FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Leishmania infantum_jpcm5FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Leishmania majorFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Leishmania mexicana_mhom_gt_2001_u1103FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Leishmania panamensisFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Leptomonas pyrrhocorisFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Leptomonas seymouriFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Lotharella oceanicaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Monosiga brevicollis_mx1FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Naegleria gruberiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Nannochloropsis gaditanaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Nannochloropsis gaditana_ccmp526FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Oxytricha trifallaxFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Oxytricha trifallax_gca_000295675FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Paramecium tetraureliaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Paulinella chromatophoraFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Perkinsela sp_ccap_1560_4FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Perkinsus marinus_atcc_50983FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Phaeodactylum tricornutumFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(otherfeatures)
TSVGTFGFF3VEP
Phytomonas sp_isolate_em1FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Phytomonas sp_isolate_hart1FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Phytophthora infestansFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(otherfeatures)
MySQL(variation)
TSVGTFGFF3GVFVCFVEP
Phytophthora kernoviaeFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Phytophthora lateralisFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Phytophthora nicotianaeFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Phytophthora nicotianae_gca_001482985FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Phytophthora parasiticaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Phytophthora parasitica_cj01a1FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Phytophthora parasitica_gca_000509465FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Phytophthora parasitica_gca_000509485FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Phytophthora parasitica_gca_000509505FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Phytophthora parasitica_gca_000509525FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Phytophthora parasitica_inra_310FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Phytophthora parasitica_p10297FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Phytophthora parasitica_p1976FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Phytophthora ramorumFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Phytophthora sojaeFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(otherfeatures)
TSVGTFGFF3VEP
Plasmodiophora brassicaeFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Plasmodium bergheiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Plasmodium berghei_gca_000005395FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium berghei_gca_900044335FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium chabaudiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Plasmodium chabaudi_chabaudiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium cynomolgi_strain_bFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium falciparumFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(variation)
TSVGTFGFF3GVFVCFVEP
Plasmodium falciparum_7g8FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium falciparum_camp_malaysiaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium falciparum_dd2FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium falciparum_fch_4FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium falciparum_hb3FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium falciparum_igh_cr14FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium falciparum_malips096_e11FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium falciparum_nf135_5_c10FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium falciparum_nf54FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium falciparum_palo_alto_ugandaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium falciparum_raj116FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium falciparum_santa_luciaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium falciparum_tanzania_2000708_FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium falciparum_ugt5_1FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium falciparum_vietnam_oak_knoll_fvo_FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium fragileFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium gaboniFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium inui_san_antonio_1FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium knowlesiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Plasmodium reichenowiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium reichenowi_gca_001601855FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium vinckei_petteriFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium vinckei_vinckeiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium vivaxFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Plasmodium vivax_brazil_iFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium vivax_india_viiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium vivax_mauritania_iFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium vivax_north_koreanFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium yoeliiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium yoelii_17xFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium yoelii_gca_900002395FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmodium yoelii_yoeliiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Plasmopara halstediiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Polysphondylium pallidum_pn500FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Pseudocohnilembus persalinusFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Pythium aphanidermatumFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Pythium arrhenomanesFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Pythium irregulareFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Pythium iwayamaiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Pythium ultimumFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(otherfeatures)
TSVGTFGFF3VEP
Pythium vexansFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Reticulomyxa filosaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Salpingoeca rosettaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Saprolegnia diclina_vs20FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Saprolegnia parasitica_cbs_223_65FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Sphaeroforma arctica_jp610FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Spironucleus salmonicidaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Strigomonas culicisFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Stylonychia lemnaeFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Tetrahymena thermophilaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Thalassiosira oceanicaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Thalassiosira oceanica_ccmp1005FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Thalassiosira pseudonanaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(otherfeatures)
TSVGTFGFF3VEP
Thecamonas trahens_atcc_50062FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Theileria annulataFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Theileria equi_strain_waFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Theileria orientalis_strain_shintokuFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Theileria parvaFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Toxoplasma gondiiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Toxoplasma gondii_ariFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Toxoplasma gondii_fouFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Toxoplasma gondii_gab2_2007_gal_dom2FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Toxoplasma gondii_gt1FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Toxoplasma gondii_masFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Toxoplasma gondii_p89FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Toxoplasma gondii_rubFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Toxoplasma gondii_tgcatprc2FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Toxoplasma gondii_vandFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Toxoplasma gondii_vegFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP
Trichomonas vaginalis_g3FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Trypanosoma bruceiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Trypanosoma cruziFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Trypanosoma cruzi_dm28cFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Trypanosoma cruzi_gca_000188675FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Trypanosoma cruzi_marinkelleiFASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Trypanosoma rangeli_sc58FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)TSVGTFGFF3VEP
Vitrella brassicaformis_ccmp3155FASTA (DNA)FASTA (cDNA)FASTA (CDS)FASTA (ncRNA)FASTA (protein)EMBLGenBankMySQL(core)
MySQL(funcgen)
TSVGTFGFF3VEP

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

Metadata

Detailed metadata on the genomes provided by Ensembl Genomes is available from the FTP site in TSV, JSON and XML formats (format details).

Ensembl Protists: TSV | JSON | XML

Ensembl Genomes (all divisions): TSV | JSON | XML

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.

MAF (comparative data)

MAF files are provided for all pairwise 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.
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