Welcome to the RNAentropy webserver !
RNA structural entropy is defined by
H = −Σ_{s} 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:

Computing expected energy <E>(s) by dynamic programing:
 Q(s) = Σ_{s} exp(E(s)/RT) · E(s)
 Z(s) = Σ_{s} exp(E(s)/RT) = partition function of s
 < E > = Q(s)/Z(s)

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) = Σ_{s} 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 GarciaMartin,Peter Clote.RNA thermodynamic structural entropy (2015) (in press)