Ensembl compara: Difference between revisions
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*** Main table '''homology''': A homology is located on a '''tree''', obtained with an (alignment/phylogenetic) '''method''', based on a '''set of species''' | *** 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''' | *** 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''' | ||
**** To select all species_sets that include rat and mouse: | |||
<pre> | |||
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"; | |||
</pre> | |||
*** | *** | ||
*** A '''homology.description''' can be ortholog or paralog and one-to-one or one-to-many, see [http://www.ensembl.org/info/docs/compara/homology_method.html Ensembl Doc], but there are also putative_gene_splits, between_species_paralogs and other_paralog | *** A '''homology.description''' can be ortholog or paralog and one-to-one or one-to-many, see [http://www.ensembl.org/info/docs/compara/homology_method.html Ensembl Doc], but there are also putative_gene_splits, between_species_paralogs and other_paralog | ||
Revision as of 10:04, 29 October 2009
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
- To 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";
- 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
