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-   -   Variant from DNA level to amino acid change level (http://seqanswers.com/forums/showthread.php?t=45728)

akitrav 08-11-2014 01:38 PM

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

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 (Post 147286)
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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