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Hi Jason<br>
<br>
You can use the HomologyAdaptor (<a class="moz-txt-link-freetext"
href="http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1DBSQL_1_1HomologyAdaptor.html">http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1DBSQL_1_1HomologyAdaptor.html</a>)
to get these relationships. You can try either the
fetch_all_by_Member_paired_species or the
fetch_all_by_Member_paired_species methods. For instance,<br>
<br>
$homology_adaptor->fetch_all_by_Member_paired_species($hsap1_member,
"mus_musculus", "ENSEMBL_ORTHOLOGUES");<br>
<br>
will return [$mmus1_member], and<br>
<br>
$homology_adaptor->fetch_all_by_Member_paired_species($hsap2_member,
"mus_musculus", "ENSEMBL_ORTHOLOGUES");<br>
<br>
will return [$mmus2_member, $mmus2'_member]. If you want to get the
intra-species paralogues as well, you can add:<br>
<br>
$homology_adaptor->fetch_all_by_Member_paired_species($hsap2_member,
"homo_sapiens", "ENSEMBL_PARALOGUES");<br>
<br>
I hope this helps<br>
<br>
Javier<br>
<br>
On 12/02/12 01:24, Jason Merkin wrote:
<blockquote
cite="mid:CANirNQtB87a5MC1uGQBiFWo=wQ1MTdZrPnV4SYP1Eo_HzresBg@mail.gmail.com"
type="cite">Hello. I am trying to identify duplications that have
occured within a group of species. I have gone through the
tutorial and the mailing list archives and couldn't find anything
on it. I will use the example on the webpage that explains the
homology definitions (<a moz-do-not-send="true"
href="http://ensembl.genomics.org.cn:8058/info/docs/compara/homology_method.html"
target="_blank">http://ensembl.genomics.org.cn:8058/info/docs/compara/homology_method.html</a>)
to illustrate what I am trying to do. Using just human and mouse,
as on the diagram, I would like to query with Hsap1 and get the
set of (Hsap1, Mmus1); query with Hsap2 and get (Hsap2, Hsap2',
Mmus2, Mmus2'); and query with Hsap3 and get (Hsap3, Mmus3,
Mmus3'). Is there a way to specify the homology type and, more
importantly, restrict the species to be considered for definining
the homology? <br clear="all">
<br>
Thanks for any help,<br>
Jason Merkin<br>
<br>
<br>
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<br>
<pre wrap="">_______________________________________________
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK</pre>
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