We show that the problem of designing RNA sequences that can fold into multiple stable secondary structures can be transformed into a combinatorial optimization problem that can be solved by means of simple heuristics. Hence it is feasible to design RNA switches with prescribed strucutral...

We study the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs. We discuss folding mechanisms and the correlation between the barrier structure of the conformational...

RNA folding is viewed as a map assigning secondary structures to sequences. At fixed chain length the number of sequences exceeds by far the number of structures. Frequencies of structures are highly non-uniform: we find relatively few common and many rare ones. Using an algorithm for inverse...

Secondary structures of polynucleotides can be view as a certain class of planar vertex-labeled graphs. We construct recursion formulae enumerating various sub-classes of these graphs as well as certain structural elements (sub-graphs). First order asymptotics are derived and their dependence on...

The heights of energy barriers separating two (macro-)states are useful for estimating transition frequencies. In non-degenerate landscapes the decomposition of a landscape into basins surrounding local minima connected by saddle points is straightforward and yields a useful definition of...

Computer codes for computation and comparison of RNA secondary structures, the {\tt Vienna RNA package}, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition...

Algorithms predicting RNA secondary structures based on different folding criteria---minimum free energy (mfe), kinetic folding (kin), maximum matching (mm)---and different parameter sets are studied systematically. Two base pairing alphabets were used: the binary GC and the natural four-letter...

An algorithm is presented for generating rigorously all suboptimal secondary structures between the minimum free energy and an arbitrary upper limit. The algorithm performs particularly well in the vicinity of the minimum free energy. This enables the efficient approximation of statistical...

We propose a new method for detecting conserved RNA secondary structures in a family of related RNA sequences. Our method is based on a combination of thermodynamic structure prediction and phylogenetic comparison. In contrast to purely phylogenetic methods, our algorithm can be used for small...

Secondary structure prediction is a standard tool in the analysis of RNA sequences. The prediction of RNA secondary structures is inherently non-local. This makes the analysis of long sequences (more than 4000 nucleotides) infeasible on present-day workstations. An implementation of the...