[Bioperl-l] Does pSW support DNA sequence?

[Ewan Birney]

On Tue, 18 Dec 2001, Jason Stajich wrote:

> 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.


I'd suggest that we move away from bioperl-cext (is neat, but not that
useful) and concentrate on wrapping EMBOSS things. I just think that's
probably stabler and easier to install.

> 
> 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...
> 

Once you've got the wrappers, building this sort of application is easy
right.... it would be nice to have it as an object.




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

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