Bioperl: NCBI 'Query' email server

[Ewan Birney]

On Tue, 18 May 1999, Simon Twigger wrote:

> Hi there,
> 
> Im in the process of planning a perl-based application which will need
> to grab nucleotide sequences from NCBI based on accession numbers and
> then take those sequences and BLAST them against one of the databases at
> NCBI, parse the results and then deal with them further. In my initial
> exploration of these ideas, I came across the NCBI query email server
> which I am thinking will be a pretty decent way to grab sequences off
> NCBI in the absence of a more direct route. (is there a more direct
> route short of mirroring the database locally?)

Actually in the current bioperl (0.05), there is all the functionality you
need (I think) already in there.

	Bio::DB::GenBank - provides http access to genbank from ncbi
	Bio::Tools::Blast - Blast sequences against a DB remotely.

I tend to use Blast locally, so I am not sure of the exact syntax, but
it would be a pretty small amout of code to write.

Try it out, and if you do have any problems in understanding the modules
or what else is happening, drop me or the guts list an email.

> --------------------------------------------------
> Simon Twigger, Ph.D.
> Laboratory for Genetic Research,
> Cardiovascular Research Center,
> Medical College of Wisconsin,
> 8701 Watertown Plank Road, 
> Milwaukee, WI, 53226
> 
> tel. 414-456-4409               fax. 414-456-6516
> --------------------------------------------------
> =========== Bioperl Project Mailing List Message Footer =======
> Project URL: http://bio.perl.org/
> For info about how to (un)subscribe, where messages are archived, etc:
> http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html
> ====================================================================
> 

Ewan Birney
<birney@sanger.ac.uk>
http://www.sanger.ac.uk/Users/birney/

=========== Bioperl Project Mailing List Message Footer =======
Project URL: http://bio.perl.org/
For info about how to (un)subscribe, where messages are archived, etc:
http://www.techfak.uni-bielefeld.de/bcd/Perl/Bio/vsns-bcd-perl.html
====================================================================