[Bioperl-l] Does pSW support DNA sequence?

[Ewan Birney]

On Fri, 23 Nov 2001, Kun Zhang wrote:

> I tried to do pairwise alignment of two DNA sequence with pSW, but it looks 
> like only protein sequence is supported (I just replaced the protein 
> sequences with DNA sequences in the pSW.pl file in the bioperl examples 
> directory). Bl2seq can handle DNA sequences. But I was hoping that 
> Smith-Waterman algorithm provides better sensitivity. Is there any way to 
> make the pSW module work for DNA?

You can force it.

Perhaps a better solution is to download the Wise2 package from
ftp.sanger.ac.uk/pub/wise2/ - once you have compiled it there is a very
"standard" alignment tool called dnal

(which I wrote)



> 
> Kun Zhang
> Human Genetics Center
> University of Texas-Houston 
> 
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