Information-theoretic uncertainty of SCFG-modeled folding space of the non-coding RNA

RNA secondary structure ensembles define probability distributions for alternative equilibrium secondary structures of an RNA sequence. Shannon's entropy is a measure for the amount of diversity present in any ensemble. In this work, Shannon's entropy of the SCFG ensemble on an RNA sequence is derived and implemented in polynomial time for both structurally ambiguous and unambiguous grammars. Micro RNA sequences generally have low folding entropy, as previously discovered. Surprisingly, signs of significantly high folding entropy were observed in certain ncRNA families. More effective models coupled with targeted randomization tests can lead to a better insight into folding features of these families. Availability: URL 〈〈http://www.plantbio.uga.edu/∼russell/index.php?s=1&n=5&r=0〉〉.

► Shannon's entropy of RNA secondary-structure was derived and implemented under SCFG.
► MicroRNA has a low structural entropy, confirming their more deterministic fold.
► Signs of significantly high structural diversity observed for certain classes of RNA.
► Both unusually high and low structural diversity may be signals indicative of RNA function.