There are several methods that can be used to predict if a particular non-synonymous SNP is deleterious; SIFT and PolyPhen, among others. Which one to use will be up to the individual researcher and the strengths and weakness of the predictors, though the two mentioned do a pretty good job. Today’s tip will be on the web interface of PolyPhen 2 hosted at the Sunyaev lab*. Many tools and databases use PolyPhen to help predict the functional effect of a nonsynonymous SNP including PolyDoms, F-SNP (which I’ve done a tip on before), NIEHS SNPs and SeattleSNPs (which we have free tutorials on), SeattleSeq and more. Today’s tip will focus on simply using the web interface, but you can always download the program and integrate it as you see fit or use one of the databases. Along with SIFT, it’s arguably one of the most used predictors out there.
From an earlier help section describing PolyPhen:
PolyPhen (=Polymorphism Phenotyping) is an automatic tool for prediction of possible impact of an amino acid substitution on the structure and function of a human protein. This prediction is based on straightforward empirical rules which are applied to the sequence, phylogenetic and structural information characterizing the substitution