2 This directory contains a few scripts, you might find useful. They're not
5 Fold automatically converts sequence files from databanks using readseq
6 and feeds the converted sequence to RNAfold
8 b2ct.c converts the bracket notation produced by RNAfold into an '.ct' file,
9 as produced by Zukers mfold.
11 b2mt.pl perl script that converts a secondary structure in bracket notation
12 into a list of x y values that can be plotted to obtain the
13 "mountain"-representation of an RNA secondary structure. E.g.:
14 RNAfold < foo.seq | b2mt.pl | xmgr -pipe
17 produces a generalized mountain presentation and the pre postion
18 entropy as a measure of well-definedness from the base pair
19 probabilities contained in an PostScript dotplot. E.g:
20 RNAfold < foo.seq; mountain.pl dot.ps | xmgr -pipe
22 dpzoom.pl extract a portion of a dot plot produced by RNAfold -p
23 e.g.: to extract the structure of bases 7361 to 7600 from the
24 folding of a complete HIV sequence use
25 dpzoom.pl -f 7361 -l 7600 HIV_dp.ps > RRE_dp.ps
28 rotate or flip the coordinates of an RNA secondary structure plot.
29 E.g. to rotate the file foo_ss.ps by 90 degrees and get a
30 clockwise drawing (instead of the default counter-clockwise), use
31 rotate_ss.pl -a 90 -m foo_ss.ps > foo90_ss.ps
34 add reliability information to a RNA seondary structure plot
35 in the form of color annotation. The script computes the
36 "positional entropy" S(i) = - Sum p(ij) log(p(ij)) and encodes
37 it as color hue, ranging from red (low entropy, well-defined) via
38 green to blue and violet (high entropy, ill-defined). Apart
39 from the secondary structure plot the dot plot containing the
40 pair probabilities p(ij) is needed. Use as
41 replot.pl foo_ss.ps foo_dp.ps > foo_rss.ps