[Bioperl-l] Problems running remote blast

Richard Adams Richard.Adams at ed.ac.uk
Tue Feb 10 03:31:56 EST 2004

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

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


Dr Richard Adams
Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK

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

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