A Parallel Shuffled Frog Leaping Algorithm Based on Stem Regions Combinatorial Optimization for RNA Secondary Structure Prediction

Abstract

RNA Secondary Structure Prediction is an important part of the biological computing. RNA secondary structure prediction algorithms tend to have higher time and space complexity. Some swarm intelligence algorithms can also be applied to RNA secondary structure prediction on the basis of stem regions combinatorial optimization algorithm, such as genetic algorithm (GA), particle swarm optimization algorithm (PSO) and shuffled frog leaping algorithm (SFLA). And these algorithms achieved good effects. According to shuffled frog leaping algorithm in the application of RNA secondary structure prediction, this paper presents a parallel discrete shuffled frog leaping algorithm (parallel-DSFLA). This parallel algorithm can run on a distributed cluster system using the MPI programming mode. The experimental results show that the parallelDSFLA got better speed-up ratio, can improve the RNA secondary structure prediction efficiency and save time. Keywords-RNA secondary structure prediction; MPI; parallel discrete shuffled frog leaping algorithm; swarm intelligence