=========== Ensembl Release 114 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. |-- assembly_chain Chain files for mapping between species assemblies | | | |-- | |-- bamcov BAM and bigWig files derived by aligning RNASeq data to the genome | | | |-- | | | |-- genebuild | |-- bed GERP constrained element data in BED format | | | |-- ensembl_compara | | | |-- | |-- blat 2bit DNA files for use with BLAT | | | |-- dna | |-- compara TreeFam HMM families | | | |-- conservation_scores GERP constrained element data in BED format | | | | | |-- | | | |-- species_trees Newick tree format files that underlie comparative analyses | |-- data_files Alignment data files from a variety of sources | | | |-- | | | |-- | | | |-- external_feature_file | | | |-- funcgen | | | |-- rnaseq | |-- embl Annotations on genomic DNA in EMBL format | | | |-- | |-- emf Alignments in EMF format | | | |-- ensembl_compara | | | |-- homologies Gene trees and protein alignments underlying othology and paralogy | | | |-- multiple_alignments Whole genome multiple alignments with conservation scores | | | |-- | |-- fasta Sequences and annotations in FASTA format | | | |-- ancestral alleles Predictions of ancestral alleles (coordinates correspond to each extant species) | | | |-- | | | |-- cdna Transcript sequences (protein-coding and pseudogene) | |-- cds Coding sequences | |-- dna Genomic DNA | |-- dna_index Genomic DNA, compressed using bgzip, with an HTSLib index | |-- ncrna Transcript sequences (non-coding RNA) | |-- pep Translation (peptide) sequences | |-- genbank Annotations on genomic DNA in GenBank format | | | |-- | |-- gff3 Gene annotation in GFF3 format | | | |-- | |-- gtf Gene annotation in GTF format | | | |-- | |-- json Genome and annotation data in JSON format | | | |-- | |-- maf Alignment dumps in MAF format | | | |-- ensembl-compara | | | |-- multiple_alignments EPO and Pecan alignments | | | | | |-- | | | |-- pairwise_alignments LastZ pairwise alignments | | | |-- | |-- mysql MySQL database per-table text files | | | |-- General genome and annotation information | | | |-- cDNA to genome alignments | | | |-- Supplementary annotation information | | | |-- RNASeq alignments and gene models | | | |-- Probe-mapping and regulatory data | | | |-- Variation data | | | |-- ensembl_accounts Schema-only copy of the database used to manage Ensembl user accounts | | | |-- ensembl_ancestral_ Predictions of ancestral alleles | | | |-- ensembl_archive_ Data on historical Ensembl releases | | | |-- ensembl_compara_ Comparative genomics: Homology, protein families, whole genome alignments, synteny | | | |-- ensembl_metadata_ Genome and assembly data | | | |-- ensembl_ontology_ Ontologies used in Ensembl | | | |-- ensembl_production_ Controlled vocabularies for Ensembl databases | | | |-- ensembl_stable_ids_ Stable ID lookups, used in search | | | |-- ensembl_website_ Information used to build Ensembl websites | | | |-- ensembl_mart_ BioMart database for genes | | | |-- genomic_features_mart_ BioMart database for genomic annotations | | | |-- ontology_mart_ BioMart database for ontologies | | | |-- regulation_mart_ BioMart database for regulatory data | | | |-- sequence_mart_ BioMart database for DNA and amino acid sequences | | | |-- snp_mart_ BioMart database for variation data (including structural variation) | |-- ncbi_blast | | | |-- genes | | | |-- genomic | |-- new_genomes.txt Summary of new genome assemblies in this release | |-- rdf Ensembl genes and external references in RDF format | | | |-- | |-- regulation Files relating to the Ensembl Regulatory build (human and mouse only) | | | |-- | |-- removed_genomes.txt Summary of removed genome assemblies in this release | |-- renamed_genomes.txt Summary of renamed genome assemblies in this release | |-- species_EnsemblVertebrates.txt Summary of all genome assemblies in this release | |-- species_metadata_EnsemblVertebrates.json Summary of removed genome assemblies in this release | |-- species_metadata_EnsemblVertebrates.xml Summary of removed genome assemblies in this release | |-- summary.txt Genome assembly counts for this release | |-- tsv Cross references from Ensembl genes, transcripts and translations to ENA, RefSeq, and UniProt | | | |-- | |-- uniprot_report_EnsemblVertebrates.txt Summary of UniProt coverage for all genome assemblies | |-- updated_annotations.txt Summary of existing genome assemblies which have new gene annotations in this release | |-- updated_assemblies.txt Summary of existing genomes which have new assemblies in this release | |-- variation Variation data and VEP cache files | | | |-- gvf Variations in GVF format | | | | | |-- | | | |-- indexed_vep_cache Cache files for use with VEP, compressed using bgzip | | | |-- vcf Variations in VCF format | | | | | |-- | | | |-- vep Cache files for use with VEP, compressed using gzip | |-- virtual machine Ensembl virtual machine | |-- xml Gene tree and orthology files in PhyloXML and OrthoXML formats | |-- ensembl-compara | |-- homologies Gene trees and protein alignments underlying othology and paralogy