[ensembl-dev] homology

[Koray Doğan Kaya]

I try to find homologous genes for a zebrafish gene. Whhat is the problem,
isn't there any homologous genes? or the code...?

use Bio::EnsEMBL::Registry;
Bio::EnsEMBL::Registry->load_registry_from_db(
    -host => 'ensembldb.ensembl.org',
    -user => 'anonymous',
    -port => 5306);
my $member_adaptor = Bio::EnsEMBL::Registry->get_adaptor(
    'Multi','compara','Member');

# fetch a Member
# get the MemberAdaptor
my $member_adaptor =
Bio::EnsEMBL::Registry->get_adaptor('Multi','compara','Member');

# fetch a Memmy $member =
$member_adaptor->fetch_by_source_stable_id('ENSEMBLPROTEIN','ENSG00000004059');
my $member =
$member_adaptor->fetch_by_source_stable_id('ENSEMBLPEP','ENSDARP00000103634');
# print out some information about the Member
print $member->description, "\n";



my $homology_adaptor = Bio::EnsEMBL::Registry->get_adaptor('Multi',
'compara', 'Homology');
my $homologies = $homology_adaptor->fetch_all_by_Member($member);

# That will return a reference to an array with all homologies
(orthologues in
# other species and paralogues in the same one)
# Then for each homology, you can get all the Members implicated

foreach my $homology (@{$homologies}) {
  # You will find different kind of description
  # UBRH, MBRH, RHS, YoungParalogues
  # see ensembl-compara/docs/docs/schema_doc.html for more details

  print $homology->description," ", $homology->subtype,"\n";
 # And if they are defined dN and dS related values
  print " dn ", $homology->dn,"\n";
  print " ds ", $homology->ds,"\n";
  print " dnds_ratio ", $homology->dnds_ratio,"\n";
}

my $homology = $homologies->[0]; # take one of the homologies and look
into it

foreach my $member_attribute (@{$homology->get_all_Member_Attribute}) {

  # for each Member, you get information on the Member specifically and in
  # relation to the homology relation via Attribute object

  my ($member, $attribute) = @{$member_attribute};
  print (join " ", map { $member->$_ }  qw(stable_id taxon_id))."\n";
  print (join " ", map { $attribute->$_ } qw(perc_id perc_pos
perc_cov))."\n";

}




-- 
M.Sc. Koray Dogan Kaya
PhD Candidate
Bilkent University,
Department of Molecular Biology and Genetics
06800 / Ankara
Turkey
Mobile: (+90) 533 526 09 51
Office: (+90)  312 290 24 03
e-mail: kkaya at bilkent.edu.tr