Welcome to the RNAentropy webserver !

RNA structural entropy is defined by H = −Σs p(s) ln p(s), where p(s)=exp(−E(s)/RT)/Z is the Boltzmann probability of secondary structure s, and the sum is taken over all structures of a given RNA sequence a = a(1),..., a(n)

RNAentropy implements two cubic time algorithms to compute the RNA thermodynamic structural entropy:

  1. Computing expected energy <E>(s) by dynamic programing:
    • Q(s) = Σs exp(-E(s)/RT) · E(s)
    • Z(s) = Σs exp(-E(s)/RT) = partition function of s
    • < E > = Q(s)/Z(s)
  2. Computing expected energy <E>(s) by estimating d/dT ln(Z(T))
    • Q(s) = partition function(s) uncoupling formal temperature and using T+ΔT as formal temperature.
    • Z(s) = Σs exp(-E(s)/RT) = partition function of s
    • <E> = RT² · (ln Q(s)-ln Z(s))/ΔT), for very small ΔT

Structural entropy H(s)=<E>/RT + ln Z(s)


If you use RNAentropy in your work, please consider citing the following paper:

Juan Antonio Garcia-Martin,Peter Clote.RNA thermodynamic structural entropy (2015) (in press)