A Particle Swarm Optimizer (PSO) for RNA secondary structure prediction

HelixPSO is a multi swarm algorithm that searches the conformation space of an RNA sequence for low lying structures. Fitness is a combination of free energy and agreement with the centroid structure in the thermodynamic ensemble. HelixPSO has been used on sequences of up to 1500 nucleotides. The first version of the algorithm assesses fitness based on thermodynamic information alone. The extended version of the paper calculates fitness from thermodynamic information as well as centroid information.


The source code is available here.


M. Geis, M. Middendorf
A Particle Swarm Optimizer for Finding Minimum Free Energy RNA Secondary Structures.
Proc. IEEE Swarm Intelligence Symposium, IEEE, 8 pp., 2007.

Extended version:

M. Geis, M. Middendorf
Particle Swarm Optimization for Finding RNA Secondary Structures
International Journal of Intelligent Computing and Cybernetics, 4(2): 160-186, 2011.