How is the algorithm for Sfold different from other established algorithms?
• The algorithm generates a statistical sample of RNA secondary structures from the Boltzmann ensemble of RNA secondary structures. From a statistical mechanics perspective, an RNA molecule may have a population of structures distributed according to a Boltzmann distribution, which gives the probability of a secondary structure I at equilibrium as (1/U)exp[-E(I)/RT], where E(I) is the free energy of the structure, R is the gas constant, T is the absolute temperature, and U is the partition function for all admissible secondary structures of the RNA sequence. The algorithm samples secondary structures exactly and rigorously according to the Boltzmann distribution. The sampling method offers an appealing solution to the problem of uncertainties in the folding model and in the free energy parameters. For the details of the algorithm and its unique capabilities listed below, please see our cover article (Ding & Lawrence 2003, Nucleic Acids Res. 31, 7280-7301).
