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-   -   How to get the mutated protein sequence from the DNA mutation information? (http://seqanswers.com/forums/showthread.php?t=45194)

lix 07-22-2014 11:44 PM

How to get the mutated protein sequence from the DNA mutation information?
 
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 certain length) in batch?

Many thanks.

Matt Kearse 07-24-2014 12:05 AM

Geneious can do it although it's commercial software. There is probably some free software out there to do it, but I'm not aware of any.

A year or two ago I heard (and this might be wrong) that Geneious was the only software that correctly calls phased amino acid effects when for example only the first and third position in a codon have SNPs. You can watch a 30 second demo of this at https://www.youtube.com/watch?v=IOGmxjK3f_4#t=2m57s

Jeremy 07-24-2014 01:04 AM

Check out the program SNPeff (http://snpeff.sourceforge.net/).

lix 07-24-2014 06:00 PM

Jeremy, thanks. I basically checked SNPeff and it looks it can tell how the amino acid changes, and output the length of the changed amino acids length.

I wonder whether SNPeff has the choice to control the length of amino acids length output. Say, N amino-acid-length centered with the mutation and we can control the "N" before SNPeff automatically generated the mutated amino acids length.


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