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<p><span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">Hi,</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">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.</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">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: </span><a href="http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1DBSQL_1_1MethodLinkSpeciesSetAdaptor.html#aeb42739559569b62ee3bfab6da764976?" target="_blank" style="font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1DBSQL_1_1MethodLinkSpeciesSetAdaptor.html#aeb42739559569b62ee3bfab6da764976?</a><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">my question is what would be a script to retrieve such data? Help please. Thank
you</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">use strict;</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">use warnings;</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">use Bio::EnsEMBL::Registry;</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">## Load the registry automatically</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">my $reg = "Bio::EnsEMBL::Registry";</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">$reg->load_registry_from_url('mysql://anonymous@ensembldb.ensembl.org');</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">## Get the compara mlss adaptor</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">my $mlss_adaptor = $reg->get_adaptor("Multi", "compara", "MethodLinkSpeciesSet");</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">## Get the compara homology adaptor</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">my $homology_adaptor = $reg->get_adaptor("Multi", "compara", "Homology");</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">## Species definition</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">my $species1 = 'human';</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">my $species2 = 'mouse';</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">## Get the MethodLinkSpeciesSet object describing the orthology between the two
species</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);"><strong>my $this_mlss = $mlss_adaptor->fetch_by_method_link_type_registry_aliases('ENSEMBL_ORTHOLOGUES',
[$species1, $species2]);</strong></span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">## Get all the homologues</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">my $all_homologies = $homology_adaptor->fetch_all_by_MethodLinkSpeciesSet($this_mlss);</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">## For each homology</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">my $count = 0;</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">foreach my $this_homology (@{$all_homologies}) {</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);"> ## only keeps the one2one</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);"> if ($this_homology->description() eq 'ortholog_one2one') {</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);"> $count++;</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);"> }</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">}</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">print "There are $count 1-to-1 orthologues between $species1 and $species2\n";</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">## Alternative (shorter) version</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">my $all_one2one = $homology_adaptor->fetch_all_by_MethodLinkSpeciesSet($this_mlss,
-orthology_type => 'ortholog_one2one');</span><br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<br style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">
<span style="color: rgb(33, 33, 33); font-family: 'Segoe UI', 'Segoe WP', 'Segoe UI WPC', Tahoma, Arial, sans-serif; font-size: 13.3333px; background-color: rgb(255, 255, 255);">print "It should be the same number as: ", scalar(@{$all_one2one}), "\n";</span><br>
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