# -*-Text-*-
This directory contains a few scripts, you might find useful. They're not 
installed by default.

Fold	automatically converts sequence files from databanks using readseq
	and feeds the converted sequence to RNAfold

b2ct.c  converts the bracket notation produced by RNAfold into an '.ct' file,
	as produced by Zukers mfold.

b2mt.pl	perl script that converts a secondary structure in bracket notation 
	into a list of x y values that can be plotted to obtain the 
	"mountain"-representation of an RNA secondary structure. E.g.:
	RNAfold < foo.seq | b2mt.pl | xmgr -pipe

mountain.pl
	produces a generalized mountain presentation and the pre postion
	entropy as a measure of well-definedness from the base pair 
	probabilities contained in an PostScript dotplot. E.g:
	RNAfold < foo.seq; mountain.pl dot.ps | xmgr -pipe

dpzoom.pl	extract a portion of a dot plot produced by RNAfold -p
	e.g.: to extract the structure of bases 7361 to 7600 from the
	folding of a complete HIV sequence use
		dpzoom.pl -f 7361 -l 7600 HIV_dp.ps > RRE_dp.ps
	
rotate_ss.pl
	rotate or flip the coordinates of an RNA secondary structure plot.
	E.g. to rotate the file foo_ss.ps by 90 degrees and get a
	clockwise drawing (instead of the default counter-clockwise), use
	        rotate_ss.pl -a 90 -m foo_ss.ps >  foo90_ss.ps

relplot.pl
	add reliability information to a RNA seondary structure plot
	in the form of color annotation. The script computes the 
	"positional entropy" S(i) = - Sum p(ij) log(p(ij)) and encodes
	it as color hue, ranging from red (low entropy, well-defined) via
	green to blue and violet (high entropy, ill-defined). Apart
	from the secondary structure plot the dot plot containing the
	pair probabilities p(ij) is needed. Use as
	        replot.pl foo_ss.ps foo_dp.ps > foo_rss.ps