How To Check If The Iupac Snp Code Changes Translation ?

Question

[jvijai]

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

Answer 1

[Pierre Lindenbaum]

You can try

• SIFT
• polyphen
• Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
• ...

[jvijai]

Thank you. I will check them all.

[jvijai]

BTW: first link leads to sitedown ! :P

[Pierre Lindenbaum]

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

[Bioinfosm]

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?

[Pierre Lindenbaum]

@bioinfosm Here

Answer 2

[Louis Letourneau]

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.

[jvijai]

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

Answer 3

[Larry_Parnell]

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.