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

[Jason Stajich]

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