<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 12pt;
font-family:Calibri
}
--></style></head>
<body class='hmmessage'><div dir='ltr'><div><div>Hi,</div><div><br></div><div><br></div><div>I am trying to find a way for aligning all orthologs proteins from 18 mammals species to human proteins.</div><div><br></div><div>I've read the <a href="http://asia.ensembl.org/info/docs/compara/homology_method.html">Gene Orthology/Paralogy prediction method</a>.</div><div><br></div><div>In the step 4 of this pipeline, for each cluster of genes (clustering based on their Blast scores), they've built multiple alignments using protein sequences .</div><div><br></div></div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;"><div><div><i>For each cluster, build a multiple alignment based on the protein sequences using a combination of multiple aligners, consensified by M-Coffee</i></div></div></blockquote><div><div><br></div><div>All the aligments are available here in <a href="ftp://ftp.ensembl.org/pub/release-71/emf/ensembl-compara/homologies/Compara.71.protein.aa.fasta.gz">FASTA format</a> or in <a href="ftp://ftp.ensembl.org/pub/release-71/emf/ensembl-compara/homologies/Compara.71.protein.aln.emf.gz">EMF format</a>.</div><div>I've downloaded those data. Then, I've filtered out all protein sequences that don't belong to one of the 18 mammals species on which I'm focused. <br><span style="font-size: 12pt;">Still, my problem remains now with the paralogs proteins. I can't get rid off those efficiently.<br><br>For one of the alignment, I have those <b>mammal species GI|Human Orthologs GI</b> (if Human Orthologs exists) :</span></div><div><span style="font-size: 12pt;"><br>ENSBTAG00000001468|ENSG00000020577</span></div><div><span style="font-size: 12pt;"><div>ENSBTAG00000009785|ENSG00000179134</div><div>ENSCAFG00000005568|ENSG00000179134</div><div>ENSCAFG00000014940|ENSG00000020577</div><div>ENSECAG00000010681|ENSG00000020577</div><div>ENSECAG00000015551|ENSG00000179134</div><div>ENSFCAG00000010739|ENSG00000179134</div><div>ENSG00000020577</div><div>ENSG00000179134</div><div>ENSGGOG00000000673|ENSG00000020577</div><div>ENSGGOG00000024088|ENSG00000179134</div><div>ENSLAFG00000011957|ENSG00000179134</div><div>ENSLAFG00000013245|ENSG00000020577</div><div>ENSMODG00000011669|ENSG00000020577</div><div>ENSMODG00000013478|ENSG00000179134</div><div>ENSMPUG00000005514|ENSG00000020577</div><div>ENSMPUG00000017729|ENSG00000179134</div><div>ENSMUSG00000021838|ENSG00000020577</div><div>ENSMUSG00000037513|ENSG00000179134</div><div>ENSOCUG00000000343|ENSG00000179134</div><div>ENSOCUG00000003420|ENSG00000020577</div><div>ENSOGAG00000009678|ENSG00000020577</div><div>ENSOGAG00000032553|ENSG00000179134</div><div>ENSPPYG00000005832|ENSG00000020577</div><div>ENSPPYG00000009963|ENSG00000179134</div><div>ENSPTRG00000006364|ENSG00000020577</div><div>ENSPTRG00000010961|ENSG00000179134</div><div>ENSPVAG00000011118|ENSG00000179134</div><div>ENSPVAG00000016060|ENSG00000020577</div><div>ENSRNOG00000010489|ENSG00000020577</div><div>ENSRNOG00000019831|ENSG00000179134</div><div>ENSSSCG00000010706|ENSG00000179134</div><div>ENSSSCG00000016927|ENSG00000179134</div><div>ENSSSCG00000023408|ENSG00000020577</div><div>ENSSTOG00000003379|ENSG00000179134</div><div>ENSSTOG00000015276|ENSG00000020577</div><div>ENSTTRG00000003554|ENSG00000179134</div><div>ENSTTRG00000008280|ENSG00000020577</div><div><br>So I don't know which Human GI I should select (<span style="font-size: 12pt;"><i>ENSG00000179134</i> or<i> </i></span><span style="font-size: 12pt;"><i>ENSG00000020577</i></span><span style="font-size: 12pt;">).<br>Should I split this alignment in two ?</span></div><div><span style="font-size: 12pt;"><br></span></div><div><span style="font-size: 12pt;">My final goal would be to have one human protein aligned with at least 10 orthologs proteins from a different species out of the 18 mammals species, which I'm studying.</span></div></span></div><div><br></div><div>So I'm trying to find the best way to do it... Any suggestions ?</div><div>Am i mistaking in the way of achieving it ?</div><div><br></div><div>Best.</div><div><br></div><div>Dubreuil Benjamin</div></div> </div></body>
</html>