[Bioperl-l] AlignIO::emboss

[Jason Stajich]

Added a parser called Bio::AlignIO::emboss for reading in alignments
produced from the emboss programs water and needle.  This plugs into
AlignIO system (yah OO design) like all the rest of the parsers.

In doing this it brings up a thought about pairwise sequence alignments
(the above programs plus pSW, bl2seq) - do we want to provide Bio::Search
functionality for Bio::SimpleAlign

i.e.

I can get a bl2seq report and get Subject/HSPs, e-values, percent id, etc
through the Bio::SearchIO system (...well soon) or Bio::Tools::BPlite.

I can also get the data in a Alignment object - Bio::SimpleAlign suitable
for asking about slices of the alignment, building profiles for subsequent
searching, etc.

Should we think about some clearer mapping between these objects
(Bio::Search::HSP/ Bio::Tools::BPlite::HSP and Bio::SimpleAlign)?  In
cases of MSA it is mixing apples and oranges to try and  talk about a
HSP for the alignment, but for pairwise alignments it is reasonable to
want to know percent id, etc.

-jason

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