[Bioperl-l] Local database building
Fri, 05 Oct 2001 09:15:37 +0100
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.
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
> >orf3@contig21@8@12 35 431 Predicted orf
> 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!
> Bioperl-l mailing list
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