Bioperl: BLAST.pm

[Joseph Ryan]

Should a BLAST module be All-encompassing?  (like a CGI.pm)
or would a set of BLAST modules be better.  (like CGI::*.pms)

Here is some of the functionality I was thinking should go into the module(s).

RUN METHODS

run_local method
run_remote method  (use LWP to run against another machine (or even NCBI??))
Able to handle traditional BLAST, Gapped BLAST and PSI-BLAST

PARSE METHODS

This may be tricky because BLAST outputs are subject to change
("The BLAST report is not intended to be a parseable document. It is subject to
change with little or no notice.
http://www.ncbi.nlm.nih.gov/BLAST/newblast.html")
This is perhaps a reason to separate a BLAST::Parse module out of the main
module.

Be able to retrieve an Array of sequences from BLAST report and get at their
source_databases, accession_numbers, locus, def_line, high_score, E-Value,
identities, etc.

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Unfortunately, my boss is not so keen on the idea of me spending a lot of time
on a module.  I am willing to spend some free time to this project.  I am
interested in seeing what functionality Chris (Dagdigian) has already built
into his module and going from there.

Joe Ryan
Programmer
National Human Genome Research Institute



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