infernal - inference of RNA secondary structure alignments
Sean Eddy (eddy@genetics.wustl.edu)
HHMI & Washington University School of Medicine, Saint Louis.

This is release 0.1 - a dysfunctional release that's only intended to
document the paper "A memory efficient dynamic programming algorithm
for optimal structural alignment of a sequence to an RNA secondary
structure", SR Eddy, BMC Bioinformatics, submitted (2002).

To build the software:
	./configure
	make

To peruse the source code:
	it's in the src/ subdirectory.
	The covariance model structure is in structs.h
	Model construction code is in modelmaker.c
	The divide and conquer algorithm is in smallcyk.c

To run examples:
	The data used to generate Table 1 in the paper are in the intro/ subdirectory.
	To gather the SSU data, for example (deal with path issues yourself; 
        executables are in the binaries/ subdir after a "make"):

	% cmbuild ssu.cm ssu.sto              [Builds model from alignment.]
        % cmscore --smallonly ssu.cm ssu.fa   [Parses/aligns E. coli SSU using model ssu.cm]
        % cmscore --scoreonly ssu.cm ssu.fa   [Scores SSU, using score-only Inside algorithm]
		

SRE, Mon Apr 29 16:02:38 2002 [St. Louis]


