The determination of the secondary structures of ribonucleic acids as a constraint satisfaction problem

The authors use the constraint satisfaction problem formalism as a basis for an interactive and iterative method for determining secondary structures. Consistency related algorithms are used and new procedures of searching are discussed which compute only saturated secondary structures. At this time, the searchRNA procedure is not a complete algorithm and work has to be continued in order to characterize valid saturated secondary structures which are not computed. Standard restrictions were encoded as constraints but other restrictions may be considered in order to compute other families of secondary structures. In the programming environment, the method is associated with the pairing probability matrix which serves as a matrix selection