Ensembl compara

Documentation on Ensembl server

• genome_db: All species in this database
• There are two different types of homologies: protein and genomic
  • Genomic homologies:
  • Protein homologies:
    • Main table homology: A homology is located on a tree, obtained with an (alignment/phylogenetic) method, based on a set of species
    • The method and the set of species (method_link_species_set_id) are a reference to method_link_species_set. This table points to method_link and to species_set
    • A homology.description can be ortholog or paralog and one-to-one or one-to-many, see Ensembl Doc, but there are also putative_gene_splits, between_species_paralogs and other_paralog