[Bioperl-l] two sequences alignment question
yanfeng at csit.fsu.edu
Mon Apr 4 01:05:31 EDT 2005
Hi, bioperl experts,
I am a bioper and perl beginner. I have two sequences. One is very long( say 16000) and the other is short( say 100) . The short one is very similar to some part of the long sequence.
I want to locate the position like from 1200 to 1300 is the very similar sequence part.
I tried to use bl2seq module.But failed. It maybe a simple question but I just don't know how to do it.
#Get 2 sequences
$str = Bio::SeqIO->new(-file=>'t/amino.fa' , '-format' => 'Fasta', );
my $seq3 = $str->next_seq();
my $seq4 = $str->next_seq();
# Run bl2seq on them
$factory = Bio::Tools::StandAloneBlast->new('program' => 'blastp',
'outfile' => 'bl2seq.out');
my $bl2seq_report = $factory->bl2seq($seq3, $seq4);
# Note that report is a Bio::SearchIO object
# Use AlignIO.pm to create a SimpleAlign object from the bl2seq report
$str = Bio::AlignIO->new(-file=> 'bl2seq.out','-format' => 'bl2seq');
$aln = $str->next_aln();
the complain imformation is "can't write to bl2seq.out.
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