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How To Check If The Iupac Snp Code Changes Translation ?

So, I have data from an exome sequencing. I also have the SNP calls from Bioscope. My question is how to check if the IUPAC codes from the variants (with Chr & Pos) changes the translation? In other words, is the exome variant functionally important as a missense/nonsense. Is there a simple way to check just one variant? Is there a way to check 1000's of variants?

thanks

exome next-gen sequencing variant
• 6,528 views • link
updated by Larry_Parnell Larry_Parnell • written by jvijai jvijai

3 answers

You can try

• 4 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Thank you. I will check them all.

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written by jvijai jvijai

BTW: first link leads to sitedown ! :P

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written by jvijai jvijai

How about doing the opposite, going from a amino acid position on a protein to a genomic coordinate? is there some tool that can do that?

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written by Bioinfosm Bioinfosm

There's SVA (SequenceVariantAnalyser) also: http://people.genome.duke.edu/~dg48/sva/howitworks.php

If you're not working on human, all these tools won't quite do the trick since they're tweak for human genomes.

We had to write our own for c. elegans, some fungus and other fun species.

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written by Louis Letourneau Louis Letourneau

Working on human, will check to see if these will be useful. Thanks

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written by jvijai jvijai

I would also add that I like to run the two versions (each allele) of the protein sequence through Pfam for two reasons:

  1. Learn if the polymorphism is within a functional domain and how the new allele affects the Pfam score.
  2. If it is, see if the alleles are more or less tolerated in the matrix and present in other taxa, and which those are (when you view the underlying multi-seq alignment behind the Pfam).

I also like SIFT and POLYPHEN.

• 2 views • link
written by Larry_Parnell Larry_Parnell

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