[Bioperl-l] BLASTing BioSeq objects

James Wasmuth james.wasmuth@ed.ac.uk
Tue, 10 Dec 2002 15:40:54 +0000

Hi all,

I'm trying to blast a sequence which is introduced to the program as a 
string all implemented as a CGI userinterface.  The sequence is in fasta 
format, though I hope to extend this to any.

I thought I had been able to create a Bio::Seq object from the string, 
which StandAloneBlast requires,  by doing...

my $stringfh = new IO::String($query_str);
my $bioSeq_obj = new Bio::Seq(-fh => $stringfh, -format => 'fasta');

however a check on the length of the sequence in the object reveals it 
to be zero in length.

Anyone any ideas?  Should I first create a SeqIO object and convert this 
to a Bio::Seq object and then BLAST.  If so, how is this conversion done?

I'm sure the answers are in the archive but have been unable to locate 

Many Thanks