[Bioperl-l] Caching sequences

Chris Fields cjfields at uiuc.edu
Fri Oct 27 11:09:36 EDT 2006


> I have a script that is capable of downloading sequences from GenBank
> based on GI numbers. I retrieve them if fasta format in order to save
> bandwidth, but I'd like to take this one step further and cache the
> sequences in case the user want to rerun the script using some of the
> GI's they used previously.
> 
> Does anyone have any guidance on how best to do this?
> 
> Cheers
> Nath

There is Bio::DB::InMemoryCache, which is really an interface but appears to
have several methods defined; you could look for modules which implement it.
Sendu's suggestion of the Bio::Index modules and bioperl-db are also good
starting points.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 




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