[Bioperl-l] results problem with StandAloneBlast

[Torsten Seemann]

> my $ref_seq_objs; # ref to array of Sequence obj's
> my $genome_seq; # fasta containing 1 genomic sequence
> my @params = ('program' => 'blastn',
> 	       'database' => $genome_seq,
 >                  );

The database parameter needs to be the same thing you would pass to the 
"-d" option in "blastall". I don't think you can pass a perl string 
here. ie. there needs to be a properly formatted set of blast indices 
for your genome sequence on the disk in the appropriate place.
See ftp://ftp.ncbi.nlm.nih.gov/blast/documents/blast.html

> my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
> my $blast_report = $factory->blastall($ref_seq_objs); #OK

But I could be wrong, and $blast_report here contains a valid BLAST report.

-- 
Dr Torsten Seemann               http://www.vicbioinformatics.com
Victorian Bioinformatics Consortium, Monash University, Australia