
<html>

<head>

<style><!--

.hmmessage P

{

margin:0px;

padding:0px

}

body.hmmessage

{

font-size: 10pt;

font-family:微软雅黑

}

--></style></head>

<body class='hmmessage'><div dir='ltr'>

Hi All.<br><br>Sorry to bother you. I'm trying to use ensembl-compara (database version 67) to extract the homologues. I also want to get the dN, dS and dN/dS. However, ENSEMBL can't output these values. Can anyone help me? <br><br>The following is the script I used:<br><br>use Bio::EnsEMBL::Registry;<br>my $registry = 'Bio::EnsEMBL::Registry';<br>$registry->load_registry_from_db(<br>      -host       =>'ensembldb.ensembl.org',<br>      -user       =>'anonymous',<br>      -db_version =>'67');<br>my $member_adaptor=$registry->get_adaptor('Multi','compara','Member');<br>my $member=$member_adaptor->fetch_by_source_stable_id('ENSEMBLGENE','FBgn0002780');<br>my $homology_adaptor=$registry->get_adaptor('Multi','compara','Homology');<br>my $homologies=$homology_adaptor->fetch_all_by_Member($member);<br><br>for $homology(@{$homologies}){<br>    for $mem(@{$homology->get_all_Members}){<br>        my $taxon=$mem->taxon; #check Bio::EnsEMBL::Compara::NCBITaxon for methods<br>        my $id=$mem->stable_id;<br>        print "$id\t",$taxon->taxon_id,"\t",$taxon->genus," ",$taxon->species,"\t";<br>     }<br>    print $homology->description,"\t",$homology->subtype,"\t";<br>    my $dn=$homology->dn;<br>    my $ds=$homology->ds;<br>    my $dnds=$homology->dnds_ratio;<br>    my $lnl=$homology->lnl;<br>    ($dn)?print "$dn\t$ds\t$dnds\t$lnl\n":print OUT "NA\tNA\tNA\tNA\n";<br>}<br><br><br>Wish your help! Thanks very much in advance!<br><br><br>Best, Mei<br>                                           </div></body>

</html>