Vienna RNA Utilities

The Vienna RNA package comes with a number of small utilities, many of them to manipulate the PostScript files produced by the structure prediction programs RNAfold and RNAalifold.
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 | | xmgrace -pipe
similar to, 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.
Example: | xmgrace -pipe
produces a PostScript mountain plot from a color dot plot as produced by RNAalifold -p or alidot -p. 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: >
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. >
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, RNAalifold and alidot. -s file.aln >
reads a postscript secondary structure plot as produced by RNAfold and produces a new rotated and/or mirrored structure plot. -a 30 -m >
reads a postscript secondary structure plot and a dot plot containing pair probabilities as produced by RNAfold -p, and produces a new structure plot, color annotated with reliability information in the form of either pair probabilities or positional entropy (default). >
reads a postscript dot plot as produced by RNAfold -p, and extracts the dot plot for a smaller subsequence. -f 10 -l 60 >, 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 foo.ct > foo.struct
Most Perl utilities contain embedded pod documentation. Type e.g. perldoc for detailed instructions.
Ivo Hofacker