How to get the mutated protein sequence from the DNA mutation information?

lix · 07-23-2014, 12:44 AM

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, 01:05 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, 02:04 AM

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

lix · 07-24-2014, 07:00 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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07-23-2014, 12:44 AM	#1
lix Member Location: Beijing Join Date: Sep 2009 Posts: 17	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.

07-24-2014, 01:05 AM	#2
Matt Kearse Member Location: New Zealand Join Date: Mar 2014 Posts: 20	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

07-24-2014, 02:04 AM	#3
Jeremy Senior Member Location: Pathum Thani, Thailand Join Date: Nov 2009 Posts: 190	Check out the program SNPeff (http://snpeff.sourceforge.net/).

07-24-2014, 07:00 PM	#4
lix Member Location: Beijing Join Date: Sep 2009 Posts: 17	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.