# RELPLOT

## NAME

relplot − annotate a secdonary structure plot with reliability information

## SYNOPSIS

relplot [−p] [−a] file_ss.ps file_dp.ps > file_rss.ps

## DESCRIPTION

relplot reads
an RNA secondary structure plot and a dot
plot containing pair probabilities, as produced by
`"RNAfold −p"` or `"RNAcofold
−p"`, and writes a new secondary structure
with reliability annotation to stdout. The anotation is used
to colorize the plot and can use either "positional
entropy" (default), or pair probabilities (with
−p).

Positional
entropies are computed from the pair probabilities as
`"S(i) = − Sum_i p(ij) log(p(ij))"`.
Low entropy regions have little structural flexibility and
the reliability of the predicted structure is high. High
entropy implies many structural alternatives. While these
alternatives may be functionally important, they make
structure prediction more difficult and thus less
reliable.

If the −p switch is given, the script colors base pairs by their pair probability, unpaired bases use the probability of being unpaired.

If the −a switch is given, the script colors base pairs by their accessibility, i.e. the probability of being unpaired.

Entropy (repsectively probability) is encoded as color hue, ranging from red for low entropy, well-defined regions, (high probability pairs) via yellow and green to blue and violet for regions with very high entropy (low probability).

You may have to
manually move the color legend to a convenient position.
Just edit the postscript file and change the two numbers in
the line reading `"0.1 0.1 colobar"`. Or
delete the line to remove the legend.

## AUTHOR

Ivo L. Hofacker <ivo@tbi.univie.ac.at>