[Bioperl-l] assistance with bioperl

[Antonina Iagovitina]

Here is the error message I get when I try to align a sequence to an existing
alignment. Please help
I am using Windows XP and Clustalw version1.83

 MSG:
 ERROR: Could not open sequence file (-profile) 
 No. of seqs. read = -1. No alignment!
 
use Bio::AlignIO;
use Bio::SeqIO;
use Bio::Seq;
use Bio::Tools::Run::Alignment::Clustalw;

my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
$str = Bio::AlignIO->new(-file=> 'cysprot1a.msf');
$aln = $str->next_aln();
$str1 = Bio::SeqIO->new(-file=> 'cysprot1b.fa');
$seq = $str1->next_seq();
$aln = $factory->profile_align($aln,$seq);
end