[Bioperl-l] Function that determines serious mutations

Robert Bradbury robert.bradbury at gmail.com
Fri Nov 6 12:35:22 EST 2009


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


More information about the Bioperl-l mailing list