Nonsynonymous SNP (nsSNP) discovery tools?

jpeaco02 · 11-08-2009, 08:46 AM

Hi,
I have analyzed my Illumina data using Mosaik and generated a list of SNPs using Gigabayes. I would like to look for nonsynonymous SNPs so I filtered the data to limit the analysis to SNPs within Exons (approximately 1500 SNPs). I am now trying to identify which SNPs cause amino acid substitutions (nsSNPs). Are there any analysis tools or pipelines to automate the process of SNP to amino acid substitutions calling? Any help would be greatly appreciated.
Thanks
-John

nilshomer · 11-08-2009, 02:10 PM

Quote:

Originally Posted by jpeaco02

Hi,
I have analyzed my Illumina data using Mosaik and generated a list of SNPs using Gigabayes. I would like to look for nonsynonymous SNPs so I filtered the data to limit the analysis to SNPs within Exons (approximately 1500 SNPs). I am now trying to identify which SNPs cause amino acid substitutions (nsSNPs). Are there any analysis tools or pipelines to automate the process of SNP to amino acid substitutions calling? Any help would be greatly appreciated.
Thanks
-John

We use SeqWare: http://sourceforge.net/projects/seqware/ for our whole genome human resequencing. Let me know what you choose so we can also check the other options out.

pfh · 11-08-2009, 02:13 PM

I've written some software that can do this for bacteria. Doesn't work with eukaryotes though, various scalability issues yet to be overcome. http://www.vicbioinformatics.com/software.nesoni.shtml

The approach I took was just to generate all the before and after protein sequences and look for differences. Pretty easy to do in BioPerl/BioPython/etc.

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11-08-2009, 08:46 AM	#1
jpeaco02 Junior Member Location: Toronto Join Date: Nov 2009 Posts: 1	Nonsynonymous SNP (nsSNP) discovery tools? Hi, I have analyzed my Illumina data using Mosaik and generated a list of SNPs using Gigabayes. I would like to look for nonsynonymous SNPs so I filtered the data to limit the analysis to SNPs within Exons (approximately 1500 SNPs). I am now trying to identify which SNPs cause amino acid substitutions (nsSNPs). Are there any analysis tools or pipelines to automate the process of SNP to amino acid substitutions calling? Any help would be greatly appreciated. Thanks -John

11-08-2009, 02:13 PM	#3
pfh Junior Member Location: Melbourne Join Date: May 2008 Posts: 7	I've written some software that can do this for bacteria. Doesn't work with eukaryotes though, various scalability issues yet to be overcome. http://www.vicbioinformatics.com/software.nesoni.shtml The approach I took was just to generate all the before and after protein sequences and look for differences. Pretty easy to do in BioPerl/BioPython/etc.