Experiments and Results

The Nussinov Algorithm solves the problem of RNA non-crossing secondary structure prediction by base pair maximization with input sequence. For a given sequence, Nussinov Algorithm is to calculate a structure which contains most base pairs. In this implementation, when a sequence is typed, the program will give the output of the structures and how many basepair there are or the number of maximum basepair.

Zuker Algorithm is also return a set of structures but by calculating the minimal energy. There are four matrices in Zuker, which are also shown in the program. This matrices are depended on which kind of loop they have. If in the Nussinov we consider the basepair, in the Zuker Algorithm we will consider loops in the calculation. From these loops we will know how to use the energy.

McCaskill is not about a possible structure but about the probability of all possible structures. Here we used it by providing a structure of the given sequence to see its probability. And In the program, it will aslo be shwon explicitely the probabilities of every structure.