How to get the mutated protein sequence from the DNA mutation information like the VCF or MAF file?
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7.5 years ago
bioinflix ▴ 70

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 • 7.1k views
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@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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Are you interested in a particular protein or a group of targets?

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7.5 years ago

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

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5.7 years ago

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

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