How To Check If The Iupac Snp Code Changes Translation ?
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13.9 years ago
jvijai ★ 1.2k

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 • 5.3k views
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Thank you. I will check them all.

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BTW: first link leads to sitedown ! :P

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yes, it seems down, the original paper is here: http://www.ncbi.nlm.nih.gov/pubmed/12824425

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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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@bioinfosm Here

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13.9 years ago

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

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13.9 years ago

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.

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