[Bioperl-l] Does pSW support DNA sequence?

[Jason Stajich]

Do you think there is a straightforward path to incorperating a SW DNA
alignment tool in bioperl in the same manner as pSW?  Does the necessary
functionality live in bioperl-ext or are the objects coded mostly for an
aa alphabet?  I guess you could fake it with the right matrix and gap
penalties.

One can also interface to the EMBOSS program 'water' through the
Bio::Factory::EMBOSS package - but we don't have a parser for emboss
alignment output in Bio::AlignIO yet (someone could easily write it).

Would be nice to have a tool integrated into bioperl in the same way that
pSW works so that one can do alignments of bioperl seq objects w/o having
to do the whole write to 2 separate files, run the alignment, reparse the
file...

-jason

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu