Question: Polyphen2 And Nonsense Codons
2
gravatar for Pierre Lindenbaum
3.5 years ago by
France
Pierre Lindenbaum58k wrote:

Does Polyphen2/batch ( http://genetics.bwh.harvard.edu/pph2/bgi.shtml ) skip the nonsense mutations ?

I tested it with (hg18) chr22:40053278 C/G the file pph2-snps.txt contained the nonsense mutation but the file pph2-full.txt was empty.

Am I wrong ?

ADD COMMENTlink modified 3.5 years ago by Lars Juhl Jensen8.6k • written 3.5 years ago by Pierre Lindenbaum58k
1

I think the Polyphen only considers the missense mutation in their prediction pipeline. In the dbSNP id based interface [http://genetics.bwh.harvard.edu/pph2/dbsearch.shtml ] - no results are provided for other class of SNPs.

ADD REPLYlink written 3.5 years ago by Khader Shameer14k
2
gravatar for Lars Juhl Jensen
3.5 years ago by
Copenhagen, Denmark
Lars Juhl Jensen8.6k wrote:

Considering that the title of the latest PolyPhen paper is "A method and server for predicting damaging missense mutations", I think it is safe to say that it only predicts the effect of missense mutations and not of nonsense mutations.

ADD COMMENTlink written 3.5 years ago by Lars Juhl Jensen8.6k
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