[Bioperl-l] Variation

[Heikki Lehvaslaiho]

Jonathan,

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.

Yours,

	-Heikki


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
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________