Ensembl compara: Difference between revisions

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** Protein 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'''
*** 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 [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 09:56, 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
      • 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