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

DOI

10.2991/iccsee.2013.320How to use a DOI?

Keywords

RNA secondary structure prediction, MPI, parallel discrete shuffled frog leaping algorithm, swarm intelligence

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 parallel-DSFLA got better speed-up ratio, can improve the RNA secondary structure prediction efficiency and save time.

Copyright

© 2013, the Authors. Published by Atlantis Press.

Open Access

This is an open access article distributed under the CC BY-NC license (http://creativecommons.org/licenses/by-nc/4.0/).

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TY  - CONF
AU  - Chunlei Liu
AU  - Zhenzhou Ji
AU  - Yingsen Hong
PY  - 2013/03
DA  - 2013/03
TI  - A Parallel Shuffled Frog Leaping Algorithm Based on Stem Regions Combinatorial Optimization for RNA Secondary Structure Prediction
BT  - Proceedings of the 2nd International Conference on Computer Science and Electronics Engineering (ICCSEE 2013)
PB  - Atlantis Press
SP  - 1277
EP  - 1280
SN  - 1951-6851
UR  - https://doi.org/10.2991/iccsee.2013.320
DO  - 10.2991/iccsee.2013.320
ID  - Liu2013/03
ER  -