[Bioperl-l] Variation

[Allen Day]

you can read dbsnp xml files using Bio::ClusterIO.

On Tue, 27 Apr 2004, Jonathan Manning wrote:

> 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";
> 
> Thanks,
> 
> Jon  
> 
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