[Bioperl-l] genbank mirror

Brian Osborne osborne1 at optonline.net
Tue Oct 3 23:28:06 EDT 2006


Torsten and Carlo,

Right. For some simple examples of using Bio::DB::Query::BioQuery to query a
BioSQL db take a look at Bio::DB::BioSQL::OBDA.

You may also want to take a look at NCBI's eutils API, it's quite powerful
but not local. Or the ENSEMBL API, people have set up their own local
ENSEMBL dbs. There's an example of this API here:

http://www.bioperl.org/wiki/Getting_Genomic_Sequences


Brian O.


On 10/3/06 10:58 PM, "Torsten Seemann"
<torsten.seemann at infotech.monash.edu.au> wrote:

>> 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.
> 
> Have you coinsidered bioperl-db / BioSQL ?
> 
> http://www.bioperl.org/wiki/BioPerl_db
> http://lists.open-bio.org/pipermail/biosql-l/




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