[Bioperl-l] DNA Smith-Waterman?

[Yee Man]

Hi,

        I am a newbie programmer at Stanford Human Genome Center. We are
doing some DNA sequence alignments here. Occasionally, we would like to
align DNAs using some sort of Dynamic Programming algorithm a la
Smith-Waterman. 

	I found that Ewan Birney wrote a module for protein Smith-Waterman
already. Is he going to extend it to DNA as well?

        I just wrote a very simple C program that does Smith-Waterman for
DNA sequences. It is using Matrix Space with Gotoh's Improvement. Is this
the fastest implementation you can do with Smith-Waterman?

        I know XS and Perl, so if no one is going to extend that protein
Smith-Waterman to cover DNA, I can probably insert my code to do that.
What do you guys think?

Thanks
Yee Man