Predicting RNA Secondary Structure Using a Improved BPSO Based on Stem Combination

Yi Qi

doi:10.4028/www.scientific.net/AMM.325-326.1551

Paper Titles

Rapid Search Algorithms of Local Registering Based on Decimal Tree
p.1535

A New Reptile Method for Contour Tracing Based on an Extended Freeman Code and an Alterable Window
p.1539

Motion Model Parameters Estimation for Electronic Image Stabilization Instrument
p.1543

An Improved Adaptive Unsharp Masking Image Enhancement Algorithm
p.1547

Predicting RNA Secondary Structure Using a Improved BPSO Based on Stem Combination
p.1551

A Novel Self-Embedding Watermarking Scheme for Image Tamper Detection and Recovery
p.1555

Misalignment Characteristic Analysis Based on Advanced Empirical Mode Decomposition
p.1559

Visualization Design of Data
p.1564

Fast 3-D Feature Point Detector Based on Harris
p.1567

HomeApplied Mechanics and MaterialsApplied Mechanics and Materials Vols. 325-326Predicting RNA Secondary Structure Using a...

Predicting RNA Secondary Structure Using a Improved BPSO Based on Stem Combination

Abstract:

In this paper, we present an improved BPSO to predict RNA secondary structure to improve the performance with two new strategies. First one is to reduce the searching space of PSO through super stem set construction. Second is to modify the general BPSO updating process to settle stem permutation and combination problems. The experimental results show that the new method is effective for RNA structure prediction in terms of sensitivity and specificity by different sequence datasets including simple pseudoknot.

You might also be interested in these eBooks

Manufacturing Engineering and Process II

View Preview

Info:

Periodical:

Applied Mechanics and Materials (Volumes 325-326)

Pages:

1551-1554

DOI:

https://doi.org/10.4028/www.scientific.net/AMM.325-326.1551

Citation:

Cite this paper

Online since:

June 2013

Authors:

Yi Qi

Keywords:

Particle Swarm Optimization (PSO), Prediction, RNA, Secondary Structure

Export:

RIS, BibTeX

Price:

Permissions CCC:

Request Permissions

Permissions PLS:

Request Permissions

Сopyright:

Citation:

References

[1] I. Tinoco Jr. and C. Bustamante. How RNA Folds, J. Molecular Biology, vol. 293, no. 1, pp.271-281(1999).

DOI: 10.1006/jmbi.1999.3001

Google Scholar

[2] B. Furtig, C. Richter, J. Wohnert, and H. Schwalbe. NMR spectroscopy of RNA. Chembiochem, p.936–962(2003).

DOI: 10.1002/cbic.200300700

Google Scholar

[3] M. Zuker and P. Stiegler. Optimal Computer Folding of Large RNA Sequences Using Thermodynamics and Auxiliary Information, Nucleic Acids Research, vol. 9, pp.133-148(1981).

DOI: 10.1093/nar/9.1.133

Google Scholar

[4] Chong Xing, Gang Wang, Yao Wang, Zhaohua Ji, Wei Shen, Yanchun Liang, A novel method for RNA secondary structure prediction', ICNC'11, pp.1162-1166(2011).

Google Scholar

[5] Y. N. Liu, H. Dong, H. Zhang, G. Wang, Z. Li, H. L. Chen. Prediction of RNA Secondary Structure Based on Particle Swarm Optimization, Chem. Res. Chinese Universities, vol. 27, no. 1,pp.108-112(2011).

Google Scholar

[6] Michael Geis and Martin Middendorf. A Particle Swarm Optimizer for Finding Minimum Free Energy RNA Secondary Structures, Swarm Intelligence Symposium, IEEE(2007).

DOI: 10.1109/sis.2007.368019

Google Scholar