[ensembl-dev] Dev Digest, Vol 67, Issue 4

[binit treesa]

Thanks Sarah & Will McLaren for the details.


On Fri, Jan 8, 2016 at 5:30 PM, <dev-request at ensembl.org> wrote:

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> Today's Topics:
>
>    1. SIFT score differences. (binit treesa)
>    2. Re: SIFT score differences. (Sarah Hunt)
>    3. Re: SIFT score differences. (Will McLaren)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 8 Jan 2016 11:29:57 +0530
> From: binit treesa <binit.treesa at gmail.com>
> Subject: [ensembl-dev] SIFT score differences.
> To: dev at ensembl.org
> Message-ID:
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> Tnm1JGcJ3R4mAPmVa7an8j8RX0y-tnLQT_OeOW+7L9w at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi team,
>
> Recently we found a source dbNSFP which is similar to VEP result.
>
> Usually we run VEP with variants to get the SIFT and polyphen score and its
> prediction.
> While comparing these two files, I noted that there is slight difference in
> the sift and polyphen score but the prediction remains same:
>
> The version we compared :
> dbNSFP  : it support ensembl v66
> VEP result  : VEP tool v75 (ensembl v75)
>
> It will be good if you can point out the reasons behind this score
> differences.
> Also please share the procedure to calculate the SIFT and Polyphen.
>
> Thanks,
> Treesa Binit
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> ------------------------------
>
> Message: 2
> Date: Fri, 8 Jan 2016 09:34:32 +0000
> From: Sarah Hunt <seh at ebi.ac.uk>
> Subject: Re: [ensembl-dev] SIFT score differences.
> To: Ensembl developers list <dev at ensembl.org>
> Message-ID: <568F82A8.80606 at ebi.ac.uk>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
>
>
> Hi Treesa,
>
> 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:
>
> http://www.ensembl.org/info/genome/variation/predicted_data.html
>
> 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.
>
> Best wishes,
>
> Sarah
>
> On 08/01/2016 05:59, binit treesa wrote:
> > Hi team,
> >
> > Recently we found a source dbNSFP which is similar to VEP result.
> >
> > Usually we run VEP with variants to get the SIFT and polyphen score
> > and its prediction.
> > While comparing these two files, I noted that there is slight
> > difference in the sift and polyphen score but the prediction remains
> same:
> >
> > The version we compared :
> > dbNSFP  : it support ensembl v66
> > VEP result  : VEP tool v75 (ensembl v75)
> >
> > It will be good if you can point out the reasons behind this score
> > differences.
> > Also please share the procedure to calculate the SIFT and Polyphen.
> >
> > Thanks,
> > Treesa Binit
> >
> >
> >
> > _______________________________________________
> > Dev mailing list    Dev at ensembl.org
> > Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
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> ------------------------------
>
> Message: 3
> Date: Fri, 8 Jan 2016 09:35:38 +0000
> From: Will McLaren <wm2 at ebi.ac.uk>
> Subject: Re: [ensembl-dev] SIFT score differences.
> To: Ensembl developers list <dev at ensembl.org>
> Message-ID:
>         <CAMVEDX3TvXnhKxPCB5n4dqBDqjbB4sD-ss-YaSk=
> 4S79Rnyxag at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello,
>
> Differences in scores can be accounted for by two main factors:
>
> 1) the version of SIFT used to generate the score
> 2) the sequence set used to generate the alignments behind the scores
>
> This also applies to PolyPhen scores.
>
> It is not clear to me from the dbNSFP README (1) which version of SIFT they
> use - they say "ensembl 66" as you noted, so perhaps they extracted the
> SIFT scores from Ensembl v66.
>
> For release 66, Ensembl ran SIFT version 4.0.5 using UniProtKB (release
> 2012_01, both the SwissProt and TrEMBL sets) (2); for release 75, we ran
> SIFT version 5.0.2 with UniRef90 (release 2012_11) (3).
>
> So it seems the scores presented by dbNSFP are generated by an older
> version of SIFT, and with a different protein DB.
>
> Hopefully this explains the differences for you
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
> 1: https://drive.google.com/file/d/0B60wROKy6OqccXV4UXNyNkJwNUk/view
> 2:
>
> http://may2012.archive.ensembl.org/info/docs/variation/predicted_data.html#sift
> 3:
>
> http://feb2014.archive.ensembl.org/info/genome/variation/predicted_data.html#sift
>
> On 8 January 2016 at 05:59, binit treesa <binit.treesa at gmail.com> wrote:
>
> > Hi team,
> >
> > Recently we found a source dbNSFP which is similar to VEP result.
> >
> > Usually we run VEP with variants to get the SIFT and polyphen score and
> > its prediction.
> > While comparing these two files, I noted that there is slight difference
> > in the sift and polyphen score but the prediction remains same:
> >
> > The version we compared :
> > dbNSFP  : it support ensembl v66
> > VEP result  : VEP tool v75 (ensembl v75)
> >
> > It will be good if you can point out the reasons behind this score
> > differences.
> > Also please share the procedure to calculate the SIFT and Polyphen.
> >
> > Thanks,
> > Treesa Binit
> >
> >
> > _______________________________________________
> > Dev mailing list    Dev at ensembl.org
> > Posting guidelines and subscribe/unsubscribe info:
> > http://lists.ensembl.org/mailman/listinfo/dev
> > Ensembl Blog: http://www.ensembl.info/
> >
> >
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