Prediction of RNA Secondary Structures by Genetic Algorithms

Many methods can be used to predict the secondary structure of an RNA molecule. One of the methods is the dynamic programming approach. However, the dynamic programming approach usually takes too much time. Thus, it is not very practical to solve the problem of long sequences with dynamic programming. RAGA (RNA Sequence Alignment by the Genetic Algorithm) is a genetic algorithm to align two similar sequences where the structure of one of them, the master sequence, is known and the other (slave sequence) is unknown. We can predict the structure of an RNA molecule by analyzing several homologous sequence alignments. In this paper, we add a new operation in RAGA to mutate the residues of the base pairs in the master sequence and then realign the two sequences again. Our experimental results show that our new operation yields a big improvement over other traditional operations, such as crossover and mutation, in RAGA.