[ensembl-dev] SIFT score differences.

[Sarah Hunt]

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
>
>
>
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