ftp.ensembl.org
Ensembl Release 57 Databases.
THE ENSEMBL FTP SITE
The latest data is always available via a directory prefixed "current_".
For example "current_fasta" will always point to the latest data files in FASTA format.
The FTP directory has the following basic structure, although not all information is available for each species.
|-- bed GERP constrained element data in BED format
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|-- embl Gene predictions annotated on genomic DNA slices of 1MB in EMBL format
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| |-- species
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|-- emf Alignment dumps in EMF format
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| |-- ensembl_compara * protein trees and protein multiple alignments underlying othologue/paralogue alignments
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| | |-- pecan * Pecan whole genome multiple alignments with conservation scores for selected sets
| | |-- epo * EPO whole genome multiple alignments with conservation scores for selected sets
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| |-- species_variation * resequencing data
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|-- fasta Gene Predictions in FASTA format
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| |--species
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| |-- cdna * Transcript (cDNA) predictions
| |-- dna * Genomic DNA in assembled entities
| |-- pep * Translation (peptide) predictions
| |-- rna * Non-coding RNA predictions
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|-- genbank Gene predictions annotated on genomic DNA slices of 1MB in GenBank format
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| |-- species
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|-- gtf Gene annotation in GTF format
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|-- mysql MySQL database table text dumps
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|-- core General genome annotation information
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| * Genome sequence asembly
| * Ensembl gene predictions
| * Ab initio gene predictions
| * Marker information
| * ...
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|-- otherfeatures Additional genome annotation
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| * Gene predictions based on EST information
| * ...
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|-- variation Genetic variation information
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|-- vega Manually curated gene sets
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|-- cdna cDNA to genome alignments based on the latest EMBL databases
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|-- ensembl_compara Cross-species comparative genomics data:
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| * Orthologue/paralogue predictions
| * Protein families
| * Whole genome alignments
| * Synteny information
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|-- ensembl_go Gene Ontology database
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|-- ensembl_web_user_db SQL table definition for server-side user config database
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|-- ensembl_website Ensembl web site database
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| * Context-sensitive help articles
| * News articles
| * Mini-ads
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|-- ensembl-mart Cross-species data mining tables
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|-- genomic_features_mart Clone data sets
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|-- ontology_mart
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|-- sequence_mart Genome sequences
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|-- snp_mart Genetic variation information
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|-- vega_mart Manually curated gene sets
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