I have identified nonsynonymous mutation occurs on the contig position 1000 substitution by G/A through variant effect predictor. I got the transcript id & protein id and sequences of them. Now I am trying to know whether my SNP is neutral or deleterious, I am trying to use polyphen2, but it ask for the position in the amino acid sequence. How to correctly specify the substitution position in protein sequence which obtained from contig position.?
You can directly use the contig as input in Mutation Taster Translate the contig and align with protein sequence, will help u to find the amino acid position in the protein.
For functional analysis of nsSNP
a) HANSA (From our lab),
Hope this helps
If you need to extract the protein coordinates for your mutations, Oncotator tool might be helpful -- it will also provide you some extra annotation.
For testing functional impact, there is also Mutation Assessor.
Use snpEff to annotate your VCF file. In case of nonsynonymous mutation, it gives you the position of amino acid that has changed along with the before-after amino acids. I think that information can be fed into Polyphen2.