<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<br>
Hi Treesa,<br>
<br>
<meta http-equiv="content-type" content="text/html;
charset=windows-1252">
SIFT and PolyPhen results are heavily dependant on sequence
conservation estimates derived from the protein sequence alignments
and using different versions of the protein databases can result in
substantial variance in the predictions and scores obtained. We
follow the standard process for running each tool locally and
document the code and protein database versions used for each
release here:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/genome/variation/predicted_data.html">http://www.ensembl.org/info/genome/variation/predicted_data.html</a><br>
<br>
The code and protein database versions have changed a number of
times between e!66 and e!75, so I would expect many slight
differences in scores and some differences in predictions.<br>
<br>
Best wishes,<br>
<br>
Sarah<br>
<br>
<div class="moz-cite-prefix">On 08/01/2016 05:59, binit treesa
wrote:<br>
</div>
<blockquote
cite="mid:20160108060020.8E378133D4B_68F5074B@hx-mx2.ebi.ac.uk"
type="cite">
<div dir="ltr">
<div>Hi team,<br>
<br>
</div>
<div>Recently we found a source dbNSFP which is similar to VEP
result.<br>
<br>
</div>
<div>Usually we run VEP with variants to get the SIFT and
polyphen score and its prediction.<br>
</div>
<div>While comparing these two files, I noted that there is
slight difference in the sift and polyphen score but the
prediction remains same:<br>
<br>
</div>
<div>The version we compared :<br>
dbNSFP : it support ensembl v66<br>
</div>
<div>VEP result : VEP tool v75 (ensembl v75)<br>
<br>
</div>
<div>It will be good if you can point out the reasons behind
this score differences.<br>
</div>
<div>Also please share the procedure to calculate the SIFT and
Polyphen.<br>
<br>
</div>
<div>Thanks,<br>
</div>
<div>Treesa Binit<br>
<br>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</body>
</html>