Bioperl: blast_seq issues

[James Diggans]

Hello, I really hope this doesn't turn out to be a foolish question but
it's really bothering me. I recently installed bioperl 0.05 on our SGI
machine here (w/ perl 5.005) and am trying to do very simple
blasting/parsing using the blast_seq.pl script straight from the
examples directory with only the required customization. It seems to
work for the most part, returning the properly formatted html pages,
etc. However, even when including the -vers 2 flag to try and force
blast2 on all pages, the first fasta sequence to go out reads:

>BLASTing sequence 1PBH02
>Sending sequence 1PBH02 to blast server.
>(Prog=BLASTX, Version=2, DB=nr, Return=www)
>Be patient, especially during peak hours :-)...

And the output file looks fine, etc. However, on each and every
subsequent fasta file sent for blasting (-seqs option passed in a file
containing multiple sequences) the output reads:

>BLASTing sequence 1PBH02
>Sending sequence 1PBH02 to blast server.
>(Prog=BLASTX, Version=custom_server, DB=nr, Return=www)
>Be patient, especially during peak hours :-)...

And all my output file names are given 'custom_server' addendums instead
of the requested version 2. 

On top of that, when the parser output prints, 90% of the fields read
"UNKNOWN" ... what am I doing wrong? Thanks for any assistance ...
here's the command line used:

perl blast_seq.pl -seq PBerg.fasta.screen -eid -prog blastx -db nr -v 5
-b 5 -html -vers 2

I'm fairly new to bioinformatics so take it easy on me :)


- James
 
****************************************************************************
*    James C. Diggans                 
jdiggans@genomics.biotech.ufl.edu   *
*    UF ICBR Protein Expression Core  
http://genomics.biotech.ufl.edu     *
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