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Changes  view on Meta::CPAN

0.505   Fri Jul 1 16:10:52 2011
	- naming corrections
        - documentation update

0.501   Sat May 7 14:02:02 2011
	- compute_confidence_score(): boolean variables restored
        - corrected version bug

0.5   Fri May 6 12:46:25 2011
	- First Beta Release
        - _get_ens_id(): added cygid option to deal with embedded yeast ids
        - merged get_ensembl_id_from_ensembl() and get_ensembl_id_from_uniprot()
        - merged all duplicates between the pacakges: Bio::Homology::InterologWalk and
          Bio::Homology::InterologWalk::Direct
        - get_direct_interactions(): rewritten and moved to Bio::Homology::InterologWalk
        - removed Bio:Homology::InterologWalk::Direct package. All unmerged subroutines moved to
          Bio::Homology::InterologWalk
        - get_interactions(): rewritted to gather 'properties' field from MITAB data
        - get_backward_orthologies(): rewritten to use 'properties' field from MITAB data 
        - _clean_ids(): removed

lib/Bio/Homology/InterologWalk.pm  view on Meta::CPAN

                    $gene = $source_species_gene_adaptor->fetch_by_display_label($ID);
               }
               if($gene){
                    push(@genes,$gene);
               }else{
                    @genes = @{$source_species_gene_adaptor->fetch_all_by_external_name($ID)};
               }

               foreach my $gene (@genes){
                    my $all_homologies;
                    my $gid = $gene->stable_id;
                    my $member = $member_adaptor->fetch_by_source_stable_id("ENSEMBLGENE", $gid);
               
                    if (defined $member){
                         if($destorg eq "All"){ #all destination genomes
                              $all_homologies = $homology_adaptor->fetch_all_by_Member($member);
                         }else{ #one destination genome
                              $all_homologies = $homology_adaptor->fetch_all_by_Member_MethodLinkSpeciesSet($member, $orthologues_mlss);
                         }
                    }else{
                         print "$gid ..no member object defined in Ensembl, skipping..\n";
                         next;
                    }
                    next if (scalar(@$all_homologies) == 0);
                    
                    print $gid, " ", ($gene->external_name || '-'), "\t";
                    $counter = _process_homologies(homology_query_id    =>    $gid, 
                                                   homology_vector       =>   $all_homologies, 
                                                   protein_adaptor       =>   $proteintree_adaptor,
                                                   outfile               =>   $out_data,
                                                   hq_only               =>   $onetoone_only
                                                   );
                    print "..$counter orthologue(s).\n";
                    $counter_db += $counter;
               }
          }
          print "Found $counter_db orthologues in database: $ensembl_db\n";

scripts/Data/psi-mi.obo  view on Meta::CPAN

[Term]
id: MI:0034
name: display technology
def: "All the methods that permit the physical linking of a protein/peptide to its coding sequence. As a consequence affinity purification of the displayed peptide results in the genetic enrichment of its coding sequence. By these technologies genes ...
subset: PSI-MI slim
is_a: MI:0400 ! affinity technology

[Term]
id: MI:0035
name: docking
def: "Predicts the structure of a molecular complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid o...
subset: PSI-MI slim
is_a: MI:0105 ! structure based prediction
is_a: MI:0577 ! feature prediction from structure

[Term]
id: MI:0036
name: domain fusion
def: "The rosetta stone, or domain fusion procedure, is based on the assumption that proteins whose homologues in other organisms happen to be fused into a single protein chain are likely to interact or to be functionally related." [PMID:10573422]
subset: PSI-MI slim
synonym: "Rosetta Stone" EXACT PSI-MI-alternate []