Question: How to get the mutated protein sequence from the DNA mutation information like the VCF or MAF file?
6
gravatar for bioinflix
5.0 years ago by
bioinflix60
China
bioinflix60 wrote:

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.

ADD COMMENTlink modified 3.2 years ago by eric.audemard10 • written 5.0 years ago by bioinflix60

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

ADD REPLYlink written 4.9 years ago by Ammu50

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

ADD REPLYlink written 3.2 years ago by Ibrahim Tanyalcin980
2
gravatar for Sebastian Boegel
5.0 years ago by
Germany
Sebastian Boegel460 wrote:

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 COMMENTlink written 5.0 years ago by Sebastian Boegel460

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

ADD REPLYlink written 5.0 years ago by bioinflix60
1
gravatar for eric.audemard
3.2 years ago by
eric.audemard10 wrote:

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

ADD COMMENTlink written 3.2 years ago by eric.audemard10
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