Question

Prediction Tools For Snps - Grantham Scores And Phylop

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11.5 years ago

NB ▴ 960

Hello,

I am trying to prioritise my human SNP list based on prediction tools using grantham, phylop, SIFT and polyphen.

But I am not able to find much information on grantham scores and phylop, does anyone know about the sensitivity and specificity or false negative error and false positive error ( as well as the range) of Grantham score and PhyloP ?

Thank you!

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ADD COMMENT • link updated 11.5 years ago by Ashutosh Pandey 12k • written 11.5 years ago by NB ▴ 960

score 0 · Answer 1 · 2012-11-27

I am not sure if it will answer your question but recently I predicted impact of Non synonymous mutation in a particular strain of mouse using Polyphen and Grantham matrix score. There were around 12000 Non Synonymous mutation. Below is the distribution:

Grantham

593 radical (High) 1412 Moderately radical (Med) 5489 mod conservative (low) 4485 conservative (low)

Polyphen

173 unknown (Effect unknown) 8090benign (Low) 1472possibly damaging (High) 2254probably damaging (med)

You can see Grantham scores were quiet conservative. Polyphen predicted more damaging SNPs than Grantham score.