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
    • A homology is referenced by two or more homology_members

Select all species_sets that include rat and mouse:

select * from species_set s1, species_set s2, genome_db gd1, genome_db gd2 where s1.species_set_id = s2.species_set_id and s1.genome_db_id<s2.genome_db_id and s1.genome_db_id=gd1.genome_db_id and s2.genome_db_id=gd2.genome_db_id and gd1.name="Rattus norvegicus" and gd2.name="Mus musculus";

Select all species_sets with more than one or two species:

select species_set_id, count(*) as count from species_set group by species_set_id having count<>1 and count<>2;