## Welcome to the RNAlocopt webserver !

The `RNAlocopt` web server computes the Boltzmann partition function
of the set of *locally optimal* secondary structures of a given RNA
sequence. The nearest neighbor energy model with
Turner99
energy parameters are used.
(See also
NNDB: Turner99
energy parameters .)
A *locally optimal* secondary structure
has the property that the free energy cannot be decreased by adding or
removing a single basepair (contrary to intuition, there are cases where the
free energy is lowered by the removal of a base pair). The `RNAlocopt`
algorithm runs in cubic time O(n^{3}) with quadratic
O(n^{2}) space requirements, just as in the McCaskill algorithm,
as implemented in Vienna RNA Package
RNAfold
or UNAfold.

The main application of `RNAlocopt` is to sample structures
from the low energy ensemble of locally optimal secondary structures,
stochastically sampled by from the partition function of locally optimal
structures, in a manner analogous to how
Sfold
samples from the ensemble of all secondary structures.

If you use the software or web server, please consider citing the article:

W.A. Lorenz, P. Clote.

Computing the partition function for kinetically trapped RNA secondary structures.

Public Library of Science One (PLoS ONE), (2011) PLoS ONE 6(1): e16178.

doi:10.1371/journal.pone.0016178.