[Bioperl-l] Variation

Jonathan Manning bmb9jrm at bmb.leeds.ac.uk
Tue Apr 27 08:36:30 EDT 2004

Hello Bioperlers!

Could someone save me some time and tell me if it's possible to access
NCBI variation databases using bioperl? I've parsed the 'Variation'
feature information from GenBank files, but would like to get
information such as the 'function' you can see at dbSNP- i.e.
synonymous, nonsynonymous etc. I can't see this information anywhere in
the Bio::Variation objects, though that could be me being a bit dense.

Also, the following test code (with a valid dbSNP number) doesn't work-
any idea why?

$seqDiff = Bio::Variation::SNP->new(-id=> 2256408);
$ori = $seqDiff->aa_ori();
$mut = $seqDiff->aa_mut();
print "$ori $mut \n";



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