WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / Utils / README

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+# -*-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 
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