[Bioperl-l] Bio::SimpleAlign

[Kevin Brown]

I'm working on a script that plays around with alignments of sequences
and one of the things I noticed is that the code for the match method
does not seem to actually use the start/end information when creating
the match between objects in the alignment.  Maybe I'm misunderstanding
what the alignment is supposed to hold in terms of sequence.  The
alignment objects I build up are based on the sequence of a gene and the
sequences of the primers that amplify that gene.

$alignments{$gene->id()}->add_seq(
				new Bio::LocatableSeq(
				-seq   => $seq[0]->seq(),
				-id    => $seq[0]->id(),
				-start => $start,
				-end => $start + $seq[0]->length() - 1,
				-strand => 1
			 )
);
$alignments{$gene->id()}->add_seq(
				new Bio::LocatableSeq(
				-seq   => $seq[1]->seq(),
				-id    => $seq[1]->id(),
				-start => $stop,
				-end => $stop + $seq[1]->length() - 1,
				-strand => -1
				)
);

So, you can see I input a start and stop point for the primer, but when
I use the match function all it does is match the first character of the
gene sequence to the first char of the primer sequences, then the second
gene char to the second in each primer, etc...  This doesn't seem to fit
with the documentation and seems odd that there would be holders for the
start/stop points and not use them when doing things like matching of
sequences in an alignment.