[Bioperl-l] Any interest in a Bioperl parser for the RNAMOT program?

Peter Schattner schattner@alum.mit.edu
Mon, 22 Oct 2001 09:30:36 -0700

A while back I wrote a parser to read the results of the RNAMOT program.
RNAMOT (Comput Appl Biosci 1994 Apr;10(2):211-2)  is one of the principal
deterministic programs that look for secondary structure patterns in RNA
sequence alignments.  The parser is pure perl and essentially in bioperl
format so it would be easy to contribute to the CVS repository.  On the other
hand, deterministic RNA structure models like RNAMOT  have largely been
supplamted by probabilitstic models.  Consequently, I am not sure whether the
parser would still be a useful module to anyone.

So, if there is anyone (perferably more than one) for whom an RNAMOT parser
would be a useful addition to bioperl, let me know (either directly or via
this list) and I'll formally propose to add it.  If not, that's fine and I
won't clutter the CVS repository.


PS I should note that the parser is implemented using Parse::RecDescent (which
depending on your point of view could be considered a strength or a weakness)
- it would mean that yet one more CPAN module would be added to bioperl's list
of dependencies.