[Bioperl-l] Local database building

[Heikki Lehvaslaiho]

Jason,

This should be an easy thing.  You can use either Bio::Index::Fasta which
uses dbm or you can get bioperl-db from the CVS repository which does the
same thing with mySQL as a back end.

Try Bio::Index::Fasta first. You'll find an introduction to it in
bptutorial.pl section III.1.2.

	-Heikki

Jason Raymond wrote:
> 
> Another newbie question for the group :).  I'm trying to setup a local
> database from several sets of Fasta-formatted genomes, and I'm hoping to get
> a rough step-by-step on how to do this (or where to read more on this).
> Most of this data is in the format:
> 
> >orf1@contig16@8@8 35 745 Predicted orf
> LDSIFLEF....
> >orf3@contig21@8@12 35 431 Predicted orf
> MEITAL....
> ...
> 
> would this be something that can be 'smoothly' built into a database so that
> I can later retrieve sequences with Perl scripts?  Also, as of right now I
> have about 10 different files in this format, and I would ideally like them
> all to be in one single database.  Is this feasible?
> Thanks again!
> 
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> Bioperl-l@bioperl.org
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-- 
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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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