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

[Jason Stajich]

This definitely need to go into the FAQ.

See:
http://bioperl.org/pipermail/bioperl-l/2002-February/007281.html

There is a description of how to run EMBOSS's 'water' from within
Bioperl in the FAQ
http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/FAQ?rev=1.14&cvsroot=bioperl&content-type=text/vnd.viewcvs-markup


-j
On Thu, 6 Jun 2002, Danny Yoo wrote:

> 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!
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu