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How to get the mutated protein sequence from the DNA mutation information like the VCF or MAF file?

I've got the DNA mutation information which can be in a file format like VCF or MAF. Actually what I want to look at is how the mutation influence the corresponding amino acid changes.

Are there any tools can generate the mutated protein sequences corresponding to the mutated DNA in batch?

Many thanks.

protein sequence dna mutation
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updated by Ram Ram • written by bioinflix • bioinflix

@bioinflix May I know from where you got the DNA mutation information which are in file format like VCF or MAF?

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updated by Ram Ram • written by Ammu • Ammu

Are you interested in a particular protein or a group of targets?

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written by Ibrahim Tanyalcin Ibrahim Tanyalcin

2 answers

Great question (for that reason I upvoted it). You might try the R package "CustomProDB" which takes a VCF as input and outputs a protein fasta incorporating SNVs and Indels.

http://www.bioconductor.org/packages/release/bioc/html/customProDB.html

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written by Andy Andy

Thanks a lot! That really helps a lot for me!

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written by bioinflix • bioinflix

There are also python package : pyGeno - http://pygeno.iric.ca/ I don't the pros and cons of each one.

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written by eric.audemard • eric.audemard

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