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

All genomes with their ids:

select * from genome_db;

All one-to-orthologs between genome_ids 3 and 4:

select m1.stable_id, m2.stable_id, h.description from homology as h, homology_member as hm1, homology_member as hm2, member as m1, member as m2 where h.homology_id=hm1.homology_id and h.homology_id=hm2.homology_id and hm1.member_id < hm2.member_id and m1.member_id=hm1.member_id and m2.member_id=hm2.member_id and m1.genome_db_id=3 and m2.genome_db_id=4;

Timeout.

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";

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;