[Bioperl-l] Function that determines serious mutations

Alden Huang alden.huang at gmail.com
Thu Nov 26 05:54:30 EST 2009


Hey rob,

Sorting Intolerant from Tolerant
http://sift.jcvi.org/

~alden

...a bit late, i kno; I just read you post now while cleaning the inbox

On Fri, Nov 6, 2009 at 9:35 AM, Robert Bradbury
<robert.bradbury at gmail.com> wrote:
> Is there a function in the library (or has someone written one) that can
> take a genbank entry and determine which mutations are harmful?
>
> It would be used to produce a table summary of:
>  GENE          # SNP      # BadSNP
>
> One kind of gets this from NCBI if you lookup in the "GENE" db a gene name
> and then go to the "GeneView" om dbSNP page it has the information I want
> but largely in a graphical format while I simply want numbers I can dump
> into a spreadsheet.
>
> I don't think it would be hard, fetch the gene, run through the features for
> the SNP database, figure out whether they are good or bad SNPs, accumulate
> the statistics and dump it.  I think the functions available are flexible
> enough to do it but I can't believe nobody has already done it.  It could be
> a bit more complex in that one could do an analysis to see if the mutations
> are in a conserved domain or mutations that code for Cysteine or Methionine
> (or othe potentially "critical" amino acids) but since "critical" is in the
> eye of the beholder there would have to be some kind of callback to a
> scoring function.
>
> Thanks,
> Robert
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