[Bioperl-l] genbank mirror

Brian Osborne osborne1 at optonline.net
Tue Oct 3 23:16:20 EDT 2006


Carlo,

You might want to look at the Bio::DB::Query::GenBank module:

http://www.bioperl.org/wiki/HOWTO:Beginners#Retrieving_a_sequence_from_a_dat
abase

However this works through NCBI's own eutils API, setting it up to query a
local mirror may be very difficult.


Brian O.


On 10/3/06 10:06 PM, "Carlo Lapid" <cmlapid at up.edu.ph> wrote:

> Hi,
> 
> I'm trying to set up a local mirror of a large part of the Genbank database.
> For users to access the local database, I need to create a web-based search
> tool, much like Entrez of NCBI, or SRS of EBI; that can parse the Genbank
> flat files I've downloaded based on a query entered by the user.
> 
> I'm trying to use Bioperl to create this from scratch, but I'm having a very
> hard time, especially since I want the user to have reasonable flexibility
> in customizing his search. The best that I've been able to accomplish is a
> search function that retrieves genbank sequence objects based on their
> primary IDs or accession numbers; by using the fetch method of the
> Bio::Index::GenBank module. But this doesn't help users who don't know the
> exact IDs for the sequences they want.
> 
> Can anybody suggest a way to use Bioperl to search for an ordinary word or
> phrase, like "16S gene", which could be matched against the description
> field, or the entire genbank entry? (Alternatively, is there some other
> freely available tool or software that can do this?) I've been scouring the
> Bioperl documentation, but I couldn't find anything. I just need to be
> pointed in the right direction. What I thought was a relatively simple
> problem has been driving me crazy for days; if anybody has any suggestions I
> would really, really appreciate it.
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