Variant effect prediction

Question

[wrab425]

I would like to carry out a functional effect scan across the entire set of variants present in a small genome. Until now we have been using SIFT but would prefer not to rely on a single approach. Polyphen-2 is limited to human variants. Is there anything else that uses a different approach. VEP in ENSEMBL uses SIFT but would it be easier? SNP-Eff also uses an approach based on conservation; what would be the ideal combination of these apparently overlapping approaches?

[Collin]

A little clarification might help. Are you trying to predict whether variants are functionally damaging to proteins or are pathogenic (i.e. disease related)? Also, you mention a genome, are you also trying to prioritize non-coding variants?

[wrab425]

Thanks for your reply. It is a model organism; yeast. So nothing to do with disease. I am only interested in coding variants and whether and by how much they are likely to affect protein function. I have a collection of ~ 150 sequenced strains and want to know which proteins have the largest amount of deleterious variation and where these proteins to on a protein interaction network that has already been described.