[Bioperl-l] Smith-Waterman for DNA seq in bioperl?

[Yee Man]

Thanks for your reply. I am okay with XS. My problem is more with the S-W
code. My understanding is that if you can get a matrix like DNAMAT, then 
you should be able to do DNA S-W. I am not sure whether this is easy or
not though because I only skimmed the C code. Can someone who hacked it
before tells me where I should start?

Thanks for the EMBOSS water suggestion. It should be a good tool to fall
back if it is hard to do DNA S-W in pSW module.

Regards,
Yee Man

On Sat, 24 Aug 2002, Jason Stajich wrote:

> It is a bit of XS under the hood using Bio::Tools::pSW, if you've no
> experience with it, you'll find it a bit frustrating.
> 
> If you read the bioperl FAQ you'll see we reccomend using EMBOSS's water
> for SW alignments in general and water will align DNA or protein
> sequences.
> 
> -jason
> 
> On Sat, 24 Aug 2002, Yee Man wrote:
> 
> > Folks,
> >
> > 	I am a programmer at the Stanford Genome Center. I was asked to
> > run Smith-Waterman on two DNA sequences. I am wondering if it is hard to
> > make the bioperl Bio::Tools:pSW works for DNA sequences as well. If it is
> > not that hard, I think I can write a module for DNA S-W. Please give me
> > pointers on how to do this.
> >
> > Thanks in advance.
> > Yee Man
> >
> > PS Sorry for the cross-post. I posted it at bioperl-guts-l but nothing
> > seems to be happening there...
> >
> >
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> >
> 
> -- 
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>