Most Perl utilities contain embedded pod documentation. Type e.g.
- produces the mountain representation of a secondary structure
from it's bracket notation, as produced
by RNAfold. Output consists of simple x y data suitable as input to
a plotting program. The mountain representation is a xy plot with
sequence position on the x-axis and the number of base pairs
enclosing that position on the y-axis. Example:
RNAfold < my.seq | b2mt.pl | xmgrace -pipe
- similar to b2mt.pl, but produces a mountain plot from the pair
probabilities contained in a PostScript dot plot. It write 3 sets
of x y data, suitable as input for a plot program. The first two
sets containing the mountain representation from pair probabilities
and MFE structure, the third set is the "positional entropy" a
measure of structural well-definedness.
mountain.pl dot.ps | xmgrace -pipe
- produces a PostScript mountain plot from a color dot plot as
RNAalifold -p or
Each base pair is represented by a trapez whose color encodes the
number of consistent and compensatory mutations supporting that
pair: Red marks pairs with no sequence variation; ochre, green,
turquoise, blue, and violet mark pairs with 2,3,4,5,6 different
types of pairs, respectively. Example:
cmount.pl alidot.ps > cmount.ps
- reads a consensus secondary structure plot and a color dot plot
as produced by
RNAalifold -p, and writes a new
secondary structure plot in which base pairs a colored using the
color information from the dot plot.
colorrna.pl alirna.ps alidot.ps > colorRNA.ps
- reads a sequence alignment in CLUSTAL format and a consensus
secondary structure (which it extracts from a secondary structure
plot as produced by RNAalifold), and produces a postscript figure
of the alignment annotated using the consensus structure, coloring
base pair using the same color scheme as cmount.pl, RNAalifold and
coloraln.pl -s alirna.ps file.aln > coloraln.ps
- reads a postscript secondary structure plot as produced by
RNAfold and produces a new rotated and/or mirrored structure plot.
rotate_ss.pl -a 30 -m foo_ss.ps > foo_new_ss.ps
- reads a postscript secondary structure plot and a dot plot
containing pair probabilities as produced by
-p, and produces a new structure plot, color annotated with
reliability information in the form of either pair probabilities or
positional entropy (default).
relplot.pl foo_ss.ps foo_dp.ps > foo_rss.ps
- reads a postscript dot plot as produced by
-p, and extracts the dot plot for a smaller subsequence.
dpzoom.pl -f 10 -l 60 foo_dp.ps > foo_10-60_dps.ps
- ct2b.pl, b2ct
- These two utilities convert back and forth between secondary
structure in bracket format (as used in the Vienna package) and ct
files (as used by mfold).
RNAfold < foo.seq | b2ct > foo.ct
ct2b.pl foo.ct > foo.struct