Decomposition of RNA secondary structure

exert their function by interacting with other RNA molecules. In this work we extend previous RNA folding algorithms to allow the calculation of the free energy of interaction between short RNA molecules and their targets. Reliable predictions of RNA-RNA binding energies is crucial e.g. for the understanding of RNAi, microRNAmRNA binding, and antisense interactions. The thermodynamics of such RNA-RNA interactions can be understood as the sum of two energy contributions: (1) the energy necessary to expose the binding site for an interaction, and (2) the energy gained from hybridization [2]. Algorithm From a mathematical point of view a secondary structure is defined as a set of base pairs (i, j) where i < j. Two base pairs are compatible with a secondary structure if each base interacts with at most one other nucleotide and if no base pairs cross each other. A secondary structure can be uniquely decomposed into stems, loops, and exterior elements