[Bioperl-l] SearchIO and GCG

[Peter Kos]

Jason,

We often hear about RemoteBlast as well as StandaloneBlast using NCBI 
blastall, and sometimes WuBlast is mentioned.
Can I use SearchIO and Blast.pm for blast outputs of the Wisconsin 
Package (GCG)?
(As SeqIO can work on GCG formatted seq files as I know.)
I did not find the possible choices for the " '-format' => " in the 
SearchIO documentation, although it ought to be a list of certain 
exact strings (like "blast" or "fasta" or whatever) that the 
whichever underlying module will try to match/parse when I call

SearchIO -> new ...

I reckon. If I just write:

 '-format' => 'blast'

would it figure out whether the file is from blastall or WU-Blast or 
GCG-Blast or perhaps an HTML output downloaded from NCBI?

Or what can I do with a GCG-Blast output?

thanx
Peter
..................................................................  
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Peter B. Kos, Ph.D.
Molecular Microbiology and Genetics Lab.
Research Institute of Innovative Technology for the Earth (RITE)
9-2 Kizugawadai, Kizu-cho, Soraku-gun,
Kyoto 619-0292 JAPAN
Phone: +81-774-75-2308
Fax: +81-774-75-2321
E-mail: kos@rite.or.jp