<div dir="ltr"><div>Thanks Sarah & Will McLaren for the details.<br><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jan 8, 2016 at 5:30 PM, <span dir="ltr"><<a href="mailto:dev-request@ensembl.org" target="_blank">dev-request@ensembl.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Dev mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. SIFT score differences. (binit treesa)<br>
2. Re: SIFT score differences. (Sarah Hunt)<br>
3. Re: SIFT score differences. (Will McLaren)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 8 Jan 2016 11:29:57 +0530<br>
From: binit treesa <<a href="mailto:binit.treesa@gmail.com">binit.treesa@gmail.com</a>><br>
Subject: [ensembl-dev] SIFT score differences.<br>
To: <a href="mailto:dev@ensembl.org">dev@ensembl.org</a><br>
Message-ID:<br>
<CANFG3V=<a href="mailto:Tnm1JGcJ3R4mAPmVa7an8j8RX0y-tnLQT_OeOW%2B7L9w@mail.gmail.com">Tnm1JGcJ3R4mAPmVa7an8j8RX0y-tnLQT_OeOW+7L9w@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi team,<br>
<br>
Recently we found a source dbNSFP which is similar to VEP result.<br>
<br>
Usually we run VEP with variants to get the SIFT and polyphen score and its<br>
prediction.<br>
While comparing these two files, I noted that there is slight difference in<br>
the sift and polyphen score but the prediction remains same:<br>
<br>
The version we compared :<br>
dbNSFP : it support ensembl v66<br>
VEP result : VEP tool v75 (ensembl v75)<br>
<br>
It will be good if you can point out the reasons behind this score<br>
differences.<br>
Also please share the procedure to calculate the SIFT and Polyphen.<br>
<br>
Thanks,<br>
Treesa Binit<br>
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Message: 2<br>
Date: Fri, 8 Jan 2016 09:34:32 +0000<br>
From: Sarah Hunt <<a href="mailto:seh@ebi.ac.uk">seh@ebi.ac.uk</a>><br>
Subject: Re: [ensembl-dev] SIFT score differences.<br>
To: Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
Message-ID: <<a href="mailto:568F82A8.80606@ebi.ac.uk">568F82A8.80606@ebi.ac.uk</a>><br>
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<br>
<br>
Hi Treesa,<br>
<br>
SIFT and PolyPhen results are heavily dependant on sequence conservation<br>
estimates derived from the protein sequence alignments and using<br>
different versions of the protein databases can result in substantial<br>
variance in the predictions and scores obtained. We follow the standard<br>
process for running each tool locally and document the code and protein<br>
database versions used for each release here:<br>
<br>
<a href="http://www.ensembl.org/info/genome/variation/predicted_data.html" rel="noreferrer" target="_blank">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<br>
between e!66 and e!75, so I would expect many slight differences in<br>
scores and some differences in predictions.<br>
<br>
Best wishes,<br>
<br>
Sarah<br>
<br>
On 08/01/2016 05:59, binit treesa wrote:<br>
> Hi team,<br>
><br>
> Recently we found a source dbNSFP which is similar to VEP result.<br>
><br>
> Usually we run VEP with variants to get the SIFT and polyphen score<br>
> and its prediction.<br>
> While comparing these two files, I noted that there is slight<br>
> difference in the sift and polyphen score but the prediction remains same:<br>
><br>
> The version we compared :<br>
> dbNSFP : it support ensembl v66<br>
> VEP result : VEP tool v75 (ensembl v75)<br>
><br>
> It will be good if you can point out the reasons behind this score<br>
> differences.<br>
> Also please share the procedure to calculate the SIFT and Polyphen.<br>
><br>
> Thanks,<br>
> Treesa Binit<br>
><br>
><br>
><br>
> _______________________________________________<br>
> Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
> Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
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<br>
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<br>
Message: 3<br>
Date: Fri, 8 Jan 2016 09:35:38 +0000<br>
From: Will McLaren <<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>><br>
Subject: Re: [ensembl-dev] SIFT score differences.<br>
To: Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
Message-ID:<br>
<CAMVEDX3TvXnhKxPCB5n4dqBDqjbB4sD-ss-YaSk=<a href="mailto:4S79Rnyxag@mail.gmail.com">4S79Rnyxag@mail.gmail.com</a>><br>
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<br>
Hello,<br>
<br>
Differences in scores can be accounted for by two main factors:<br>
<br>
1) the version of SIFT used to generate the score<br>
2) the sequence set used to generate the alignments behind the scores<br>
<br>
This also applies to PolyPhen scores.<br>
<br>
It is not clear to me from the dbNSFP README (1) which version of SIFT they<br>
use - they say "ensembl 66" as you noted, so perhaps they extracted the<br>
SIFT scores from Ensembl v66.<br>
<br>
For release 66, Ensembl ran SIFT version 4.0.5 using UniProtKB (release<br>
2012_01, both the SwissProt and TrEMBL sets) (2); for release 75, we ran<br>
SIFT version 5.0.2 with UniRef90 (release 2012_11) (3).<br>
<br>
So it seems the scores presented by dbNSFP are generated by an older<br>
version of SIFT, and with a different protein DB.<br>
<br>
Hopefully this explains the differences for you<br>
<br>
Regards<br>
<br>
Will McLaren<br>
Ensembl Variation<br>
<br>
1: <a href="https://drive.google.com/file/d/0B60wROKy6OqccXV4UXNyNkJwNUk/view" rel="noreferrer" target="_blank">https://drive.google.com/file/d/0B60wROKy6OqccXV4UXNyNkJwNUk/view</a><br>
2:<br>
<a href="http://may2012.archive.ensembl.org/info/docs/variation/predicted_data.html#sift" rel="noreferrer" target="_blank">http://may2012.archive.ensembl.org/info/docs/variation/predicted_data.html#sift</a><br>
3:<br>
<a href="http://feb2014.archive.ensembl.org/info/genome/variation/predicted_data.html#sift" rel="noreferrer" target="_blank">http://feb2014.archive.ensembl.org/info/genome/variation/predicted_data.html#sift</a><br>
<br>
On 8 January 2016 at 05:59, binit treesa <<a href="mailto:binit.treesa@gmail.com">binit.treesa@gmail.com</a>> wrote:<br>
<br>
> Hi team,<br>
><br>
> Recently we found a source dbNSFP which is similar to VEP result.<br>
><br>
> Usually we run VEP with variants to get the SIFT and polyphen score and<br>
> its prediction.<br>
> While comparing these two files, I noted that there is slight difference<br>
> in the sift and polyphen score but the prediction remains same:<br>
><br>
> The version we compared :<br>
> dbNSFP : it support ensembl v66<br>
> VEP result : VEP tool v75 (ensembl v75)<br>
><br>
> It will be good if you can point out the reasons behind this score<br>
> differences.<br>
> Also please share the procedure to calculate the SIFT and Polyphen.<br>
><br>
> Thanks,<br>
> Treesa Binit<br>
><br>
><br>
> _______________________________________________<br>
> Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
> Posting guidelines and subscribe/unsubscribe info:<br>
> <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
> Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
><br>
><br>
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End of Dev Digest, Vol 67, Issue 4<br>
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</blockquote></div><br></div>