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relplot − annotate a secdonary structure plot with reliability information


   relplot [−p] [−a] >


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.


Ivo L. Hofacker <>