How to get the mutated protein sequence from the DNA mutation information like the VCF or MAF file?
2
8
Entering edit mode
10.3 years ago
bioinflix ▴ 80

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 • 8.7k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
4
Entering edit mode
10.3 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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
8.5 years ago

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

ADD COMMENT

Login before adding your answer.

Traffic: 1285 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6