[Bioperl-l] Applying pairwise Smith-Waterman on nucleotide sequences?

[Danny Yoo]

Hi everyone,

Hope this isn't a silly questions: I've been trying to get Bio::Tools::pSW
working on some nucleotide sequences I have.  I've written a small test
program:


###
use Bio::Tools::pSW;
use Bio::Seq;
my $factory = new Bio::Tools::pSW('-gap' => 12,
				  '-ext' => 2,
				 );
$factory->align_and_show(Bio::Seq->new(-seq=>"AAAC", -alphabet=>'dna'),
			 Bio::Seq->new(-seq=>"AATC", -alphabet=>'dna'),
			 STDOUT);
###


I get the following error message:

###
Warning Error
	Sequence seq1 is not typed as protein... ignoring!

Warning Error
	Sequence seq2 is not typed as protein... ignoring!

Warning Error
	Could not evaluate these sequences Sequence type [66][Dna]
Evaluation
type [65][Protein]
------------- EXCEPTION  -------------
MSG: Unable to build an alignment
STACK Bio::Tools::pSW::align_and_show
/usr/local/lib/perl5/site_perl/5.6.1/Bio/Tools/pSW.pm:339
STACK toplevel blast_test.pl:6

--------------------------------------
###


I'm getting the impression that Smith-Waterman is restricted to align only
on protein sequences.  Doh.


I'd like to do some nucleotide alignments locally --- should I be using
something like BLAST instead, or is there some variant of Smith-Waterman
that works on nucleotide sequences?


Thanks for any help!