[Bioperl-l] How do I bl2seq remotely?

[Uri David Akavia]

Hello.

I have a program which runs bl2seq locally using the following commands:

    my ($query, $sequence, $p_segments) = (@_);

    my @params = ('program' => "blastn", # We are comparing nucleotides
              'S' => "1",     # use only the plus strands
              'F' => "F",     # Do not filter the sequences, compare all 
of them
              'e' => "0.01" # Lower e-value, due to behavior of 
standalone BLAST
             );

    my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);

    my $report = $factory->bl2seq($query, $sequence);


I would like to convert this bit of code to run bl2seq remotely, since 
the results of remote and local BLAST don't match up. This seems like a 
bug in blast, not bioperl.

I haven't found out how to run bl2seq remotely - the documentation seems 
to focus on running blastn against a database remotely.

Could someone please send me the appropriate bit of code to do the exact 
same thing remotely?

Thanks,

Uri David Akavia