Question: Nonsynonymous Mutation-Contig To Amino Acid Position
2
gravatar for jackuser1979
5.8 years ago by
jackuser1979860
US
jackuser1979860 wrote:

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.?

mutation snp • 2.7k views
ADD COMMENTlink modified 5.8 years ago by Ashutosh Pandey11k • written 5.8 years ago by jackuser1979860

Title of the question is really vague. Please correct it so that people will open and read your question.

ADD REPLYlink written 5.8 years ago by aravind ramesh510

title of the question edited. Thanks

ADD REPLYlink written 5.8 years ago by jackuser1979860
2
gravatar for aravind ramesh
5.8 years ago by
India
aravind ramesh510 wrote:

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 Translating

For functional analysis of nsSNP

a) HANSA (From our lab),

b) PolyPhen

c) Mutation Taster

d) Condel

e) Panther

Hope this helps

ADD COMMENTlink written 5.8 years ago by aravind ramesh510
1
gravatar for B. Arman Aksoy
5.8 years ago by
B. Arman Aksoy1.2k
New York, NY
B. Arman Aksoy1.2k wrote:

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.

ADD COMMENTlink written 5.8 years ago by B. Arman Aksoy1.2k
1
gravatar for Ashutosh Pandey
5.8 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

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.

ADD COMMENTlink written 5.8 years ago by Ashutosh Pandey11k
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