Variant from DNA level to amino acid change level

akitrav · 08-11-2014, 01:38 PM

I have the variant information in form of the chromosomal position and allele change. I wish to translate it into the relevant amino acid change (if it is a nonsysn change). I do know how to do it but it seems like there must be something out there. Don't want to reinvent the wheel. Any suggestionss

GenoMax · 08-11-2014, 03:31 PM

Try SnpEff: http://snpeff.sourceforge.net/

swbarnes2 · 08-11-2014, 03:31 PM

Quote:

Originally Posted by akitrav

I have the variant information in form of the chromosomal position and allele change. I wish to translate it into the relevant amino acid change (if it is a nonsysn change). I do know how to do it but it seems like there must be something out there. Don't want to reinvent the wheel. Any suggestionss

There are programs like SNPEff and Annovar, and ensembl's Variant effect predictor, which will take genomic coordinates, and output differences with respect to genes and amino acids.

If you wanted to do a bit more yourself, you could used blastx to compare your DNA sequences to all potential proteins in the organism, and parse the blast output.

akitrav · 08-12-2014, 07:39 AM

Thank you folks but I was trying to do it from scratch or just use a functionality that does only that. Maybe if there were an R package or something like that?

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08-11-2014, 01:38 PM	#1
akitrav Junior Member Location: New york Join Date: Jul 2014 Posts: 5	Variant from DNA level to amino acid change level I have the variant information in form of the chromosomal position and allele change. I wish to translate it into the relevant amino acid change (if it is a nonsysn change). I do know how to do it but it seems like there must be something out there. Don't want to reinvent the wheel. Any suggestionss

08-11-2014, 03:31 PM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	Try SnpEff: http://snpeff.sourceforge.net/

08-12-2014, 07:39 AM	#4
akitrav Junior Member Location: New york Join Date: Jul 2014 Posts: 5	Thank you folks but I was trying to do it from scratch or just use a functionality that does only that. Maybe if there were an R package or something like that?