<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Matthieu,<div><br></div><div>Thanks for the reply! I will try the scripts you sent to me. </div><div><br></div><div>Shaohua <div><div><div>On Apr 17, 2012, at 3:17 PM, Matthieu Muffato wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear Shaohua<br><br>The most efficient way is probably to use the fetch_all_by_MethodLinkSpeciesSet_orthology_type() method from the HomologyAdaptor<br><br>You first have to create a MethodLinkSpeciesSet object<br>my $mlss_adaptor = $reg->get_adaptor("Multi", "compara", "MethodLinkSpeciesSet");<br>my $mlss = $mlss_adaptor->fetch_by_method_link_type_registry_aliases("ENSEMBL_PARALOGUES", ["human"]);<br>This object describes which kind of data you want, and on which species<br><br>Then, you can retrieve the homologies:<br>my $homology_adaptor = $reg->get_adaptor("Multi", "compara", "Homology");<br>my $all_paralogues = $homology_adaptor->fetch_all_by_MethodLinkSpeciesSet_orthology_type($mlss, "within_species_paralog");<br><br>This method can be extended to orthologues and to pairs of species. It is the fastest when it comes to fetch big sets of homologues<br><br>Hope this helps,<br>Matthieu<br><br>On 17/04/12 10:45, shaohua fan wrote:<br><blockquote type="cite">Dear all,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">As a newbie of Ensembl compara API, I want to ask whether there is a way to fetch all the within species paralogous genes of one specified genome by using the compara API? I have searched the former emails and Ensembl website and only found the solution for the single gene in the tutorial of compara API.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks a lot!<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">shaohua<br></blockquote></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; ">-----------------------------------------------------------------------------------</span><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; "><br></span><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; ">Shaohua Fan, Ph.D student.</span><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; "><br></span><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; ">Professor Axel Meyer's Lab</span><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; "><br></span><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; ">Department of Biology (Fach M617)</span><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; "><br></span><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; ">University of Konstanz</span><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; "><br></span><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; ">Universitaetsstrasse 10</span><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; "><br></span><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; ">D-78457 Konstanz</span><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; "><br></span><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; ">Germany</span><span class="Apple-style-span" style="font-family: Arial; font-size: 13px; "><br></span></div></div></span></span>
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