[ensembl-dev] extracting human mouse between species out paralogs

[Matthieu Muffato]

Dear Mouses,

Your description of BioMart and the API is correct but it doesn't work 
because we don't store between-species paralogs in the databases.

A solution is to make a (more complicated) script that goes through all 
the gene-trees and select in these all the human-mouse pairs that are 
not orthologues. I attach a script that should work. Let me know if you 
find any issues

Regards,
Matthieu, Ensembl Compara

On 08/10/15 00:29, Stamboulian, Mouses Hrag wrote:
> Hi,
>
>
> Im trying to extract the human mouse between species out-paralogs. I
> tried using the GUI through ensemble biomart however could not able to
> extract the needed data because when I select homo sapiens as my dataset
> and then select homologs as the attribute, in the paralogs sections I
> only have options to select the human paralogs (i.e. within species
> paralogs) however no options for between species paralogs were found.
>
>
> Furthermore I tried extracting the data through the perl API. In doing
> so I tried too modify this script (please find below). In doing so I
> tried to change the parameter at the bolded line in the code, in the
> fetch_by_method_link_type_registry_aliases(), by replacing the
> 'ENSEMBL_ORTHOLOGUES' by 'ENSEMBL_PARALOGUES' or 'ENSEMBLE_HOMOLOGUES'
> hoping it would return paralogs or all the homologs in general. However
> it failed to do that. I could not find what other parameters I could
> pass to this method instead of 'ENSEMBL_ORTHOLOGUES' , as I could not
> find it in your documentation present here:
> http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1DBSQL_1_1MethodLinkSpeciesSetAdaptor.html#aeb42739559569b62ee3bfab6da764976?
>
>
> my question is what would be a script to retrieve such data?  Help
> please. Thank you
>
>
> use strict;
> use warnings;
>
> use Bio::EnsEMBL::Registry;
>
> ## Load the registry automatically
> my $reg = "Bio::EnsEMBL::Registry";
> $reg->load_registry_from_url('mysql://anonymous@ensembldb.ensembl.org');
>
> ## Get the compara mlss adaptor
> my $mlss_adaptor = $reg->get_adaptor("Multi", "compara",
> "MethodLinkSpeciesSet");
>
> ## Get the compara homology adaptor
> my $homology_adaptor = $reg->get_adaptor("Multi", "compara", "Homology");
>
> ## Species definition
> my $species1 = 'human';
> my $species2 = 'mouse';
>
> ## Get the MethodLinkSpeciesSet object describing the orthology between
> the two species
> *my $this_mlss =
> $mlss_adaptor->fetch_by_method_link_type_registry_aliases('ENSEMBL_ORTHOLOGUES',
> [$species1, $species2]);*
>
> ## Get all the homologues
> my $all_homologies =
> $homology_adaptor->fetch_all_by_MethodLinkSpeciesSet($this_mlss);
>
> ## For each homology
> my $count = 0;
> foreach my $this_homology (@{$all_homologies}) {
>
>    ## only keeps the one2one
>    if ($this_homology->description() eq 'ortholog_one2one') {
>      $count++;
>    }
> }
>
> print "There are $count 1-to-1 orthologues between $species1 and
> $species2\n";
>
> ## Alternative (shorter) version
> my $all_one2one =
> $homology_adaptor->fetch_all_by_MethodLinkSpeciesSet($this_mlss,
> -orthology_type => 'ortholog_one2one');
>
> print "It should be the same number as: ", scalar(@{$all_one2one}), "\n";
>
>
>
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-- 
Matthieu Muffato, Ph.D.
Ensembl Compara and TreeFam Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
Room  A3-145
Phone + 44 (0) 1223 49 4631
Fax   + 44 (0) 1223 49 4468
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