SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to make best guest of protein class from protein sequence ajing Bioinformatics 3 06-04-2013 11:55 PM
Align genomic DNA sequence to protein database? rdu Bioinformatics 0 11-03-2011 08:31 PM
dna sequence to protein converter wijerasa Bioinformatics 1 01-14-2011 12:40 AM
PubMed: GeneScreen: a program for high-throughput mutation detection in DNA sequence Newsbot! Literature Watch 0 11-03-2010 11:20 AM

Reply
 
Thread Tools
Old 07-23-2014, 12:44 AM   #1
lix
Member
 
Location: Beijing

Join Date: Sep 2009
Posts: 17
Default 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.
lix is offline   Reply With Quote
Old 07-24-2014, 01:05 AM   #2
Matt Kearse
Member
 
Location: New Zealand

Join Date: Mar 2014
Posts: 20
Default

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
Matt Kearse is offline   Reply With Quote
Old 07-24-2014, 02:04 AM   #3
Jeremy
Senior Member
 
Location: Pathum Thani, Thailand

Join Date: Nov 2009
Posts: 190
Default

Check out the program SNPeff (http://snpeff.sourceforge.net/).
Jeremy is offline   Reply With Quote
Old 07-24-2014, 07:00 PM   #4
lix
Member
 
Location: Beijing

Join Date: Sep 2009
Posts: 17
Default

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.
lix is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:57 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO