[Bioperl-l] Does pSW support DNA sequence?

[Kun Zhang]

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?

Kun Zhang
Human Genetics Center
University of Texas-Houston