[Bioperl-l] pairwise alignment options

[Jason Stajich]

I've commited an example script in examples/aligntutorial.pl that
highlights how to align 2 sequences within bioperl.  This includes using
the EMBOSS programs, Ewan's pSW and the interfaces to TCoffee and
Clustalw.  StandAloneBlast -> bl2seq is illustrated but I don't output the
results to the screen because it doesn't produce SimpleAlign output
directly.  I hope to add that in once we have a good mapping between the
different types of searches.

The EMBOSS programs only work if one has them available locally (and so
only on UNIX) - we hope to add support for submitting jobs to remote
EMBOSS servers through PISE @pasteur and openBSA @EBI once those bridges
are completed and fully integrated into bioperl.  Volunteers welcomed.

Peter, hopefully this is a good description of how these objects work and
can be incorporated into the tutorial when you start adding the new
functionality in.

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