[Bioperl-l] Variation

Heikki Lehvaslaiho heikki at ebi.ac.uk
Tue Apr 27 10:15:51 EDT 2004


We do not have a way to access dbSNP. Maybe we should...

Bio::Variation objects do not retrieve anything. They are plain storage 
objects. Currently the only way to create them automatically is using 
Bio::LiveSeq modules which read an EMBL/GenBank entry to create a gene model 
which is then mutated and results written out in a Bio::Variation::SeqDiff 
object. See examples/liveseq/change_gene.pl.

You could access this information using Ensembl code base which is based on 
bioperl, but it is not easy. I can only repeate what I posted last week that 
bioperl access to EnsMart is a good idea and hopefully will be available at 
the end of summer.



On Tuesday 27 Apr 2004 12:36, 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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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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