[ensembl-dev] Ortholog "scores" in Compara

[Patrick Meidl]

hi all,

I'm trying to get all human <-> mouse orthologs from Compara, and would
like to include some sort of score for the ortholog prediction in my
dataset. reading the docs, I thought that perc_id of the Homology Member
would be the best value to use; fromt the schema documentation of
'homology_member':

perc_id     int(10)     YES         NULL
    defines the percentage of identity between both homologues

what puzzles me though is that for each pairwise homology, I get
different perc_ids from the two members; the documentation suggests that
you would expect the same value.

here is a short example code snippet:

--8<-----------------------------------------------------------------

$ensembl_registry->load_registry_from_db(
  -host => 'ensembldb.ensembl.org',
  -user => 'anonymous',
  -port => 5306
);
my $homology_adaptor = Bio::EnsEMBL::Registry->get_adaptor(
  'Multi', 'compara', 'Homology');
my $mlss_adaptor = Bio::EnsEMBL::Registry->get_adaptor(
  'Multi', 'compara', 'MethodLinkSpeciesSet');

my $mlss = $mlss_adaptor->fetch_by_method_link_type_registry_aliases(
  'ENSEMBL_ORTHOLOGUES', ['Homo sapiens', 'Mus musculus']);
my $homologies = $homology_adaptor->fetch_all_by_MethodLinkSpeciesSet($mlss);

foreach my $homology (@{ $homologies }) {
  print "-"x30, "\n";
  foreach my $member_attr (@{ $homology->get_all_Member_Attribute }) {
    my ($member, $attribute) = @{ $member_attr };
    print join("|", $member->stable_id, $attribute->perc_id), "\n";
  }
}

--8<-----------------------------------------------------------------

so my question is: what does the perc_id mean? is it a good measure for
the ortholog "score"? if not, what else should I use?

cheers

    patrick

-- 
Patrick Meidl, Mag.
Bioinformatician

Ce-M-M-
Research Centre for Molecular Medicine
of the Austrian Academy of Science

Lazarettgasse 14 / AKH BT 25.3
Vienna, Austria

room 02.205
phone +43 1 40160 70016
email pmeidl at cemm.oeaw.ac.at
web http://www.cemm.at/