[Bioperl-l] DNA Smith-Waterman?

[nkuipers]

Hello,

EMBOSS has a tool for doing Smith-Waterman protein/DNA alignments too. It's 
called water.  Go to the "Applications in EMBOSS" link at www.emboss.org.  If 
it's suitable for your application, why re-invent the wheel? :)

Cheers,

Nathanael


>===== Original Message From Yee Man <ymc@paxil.stanford.edu> =====
>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
>
>
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