[Bioperl-l] Wrong MSG using clustalW

Zhe Chen thechans at citiz.net
Fri Sep 16 06:24:27 EDT 2005

Pls Help: I want to append a new sequence to an existing MSF alignment profile. the following code is just copied from the tutorial. it still received a wrong msg. I am using WinXP system with ClustalW1.83.XP. How to solve it?
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);

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