Bioperl: NCBI 'Query' email server

[Simon Twigger]

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?)

http://www.ncbi.nlm.nih.gov/Web/Search/email.html

Consequently, Im looking at writing some perl to handle the 'Query'
related code - formulating the query from supplied accession numbers,
parsing the results of a 'Query' query (this can get confusing) and
passing these on to downstream applications. I'll be writing this as a
perl module and I was wondering if this sort of thing is of interest to
bio-perl and if so how it might fit in with other projects you have
going. I was thinking of using the bio::seq objects for the returned
sequences and then going on to use bio::tools::blast.pm for dealing with
the blast side of things rather than reinventing the wheel.

I would be grateful for any ideas you all may have on this and if this
can assist the overall bio-perl goal, I'd welcome any suggestions on how
best to achieve this.

Many thanks,

	Simon.


-- 
--------------------------------------------------
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
====================================================================