[Bioperl-l] Problems running remote blast

[Richard Adams]

Hi,
First of all make a sequence object :

my $seqobj = Bio::PrimarySeq->new(-seq=> $your_Sequence_String, 
-display_id => 'whatever');

Then use the synopsis from Bio::Tools::Run::RemoteBlast which is a 
minimal remote blasting module (changing
parameters as appropriate).
     
    The result that is returned in $result can be written in HTML

        my $result = $rc->next_result();


         my $writerhtml = new Bio::SearchIO::Writer::HTMLResultWriter();
         my $outhtml = new Bio::SearchIO(-writer => $writerhtml,
                                                                  
-file   => ">searchio.html");
                             # get a result from Bio::SearchIO parsing 
or build it up in memory
                            $outhtml->write_result($result);

The SearchIO modules are clearly explained in a HOWTO document if you 
want to know more.

Cheers
Richard

-- 
Dr Richard Adams
Bioinformatician,
Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK
EH4 2XU

Tel: 44 131 651 1084
richard.adams at ed.ac.uk