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A study of different annealing schedules in SARNA-predict: A permutation based SA algorithm for RNA folding

Herbert H. Tsang (Applied Research Lab, Trinity Western University, Langley, Canada)
Kay C. Wiese (School of Computing Science, Simon Fraser University, Surrey, Canada)

International Journal of Intelligent Computing and Cybernetics

ISSN: 1756-378X

Article publication date: 8 June 2015

Abstract

Purpose

The purpose of this paper is to present a study of the effect of different types of annealing schedules for a ribonucleic acid (RNA) secondary structure prediction algorithm based on simulated annealing (SA).

Design/methodology/approach

An RNA folding algorithm was implemented that assembles the final structure from potential substructures (helixes). Structures are encoded as a permutation of helixes. An SA searches this space of permutations. Parameters and annealing schedules were studied and fine-tuned to optimize algorithm performance.

Findings

In comparing with mfold, the SA algorithm shows comparable results (in terms of F-measure) even with a less sophisticated thermodynamic model. In terms of average specificity, the SA algorithm has provided surpassing results.

Research limitations/implications

Most of the underlying thermodynamic models are too simplistic and incomplete to accurately model the free energy for larger structures. This is the largest limitation of free energy-based RNA folding algorithms in general.

Practical implications

The algorithm offers a different approach that can be used in practice to fold RNA sequences quickly.

Originality/value

The algorithm is one of only two SA-based RNA folding algorithms. The authors use a very different encoding, based on permutation of candidate helixes. The in depth study of annealing schedules and other parameters makes the algorithm a strong contender. Another benefit is that new thermodynamic models can be incorporated with relative ease (which is not the case for algorithms based on dynamic programming).

Keywords

Acknowledgements

The first author would like to acknowledge support from the School of Computing Science of Simon Fraser University and a Natural Sciences and Engineering Research Council of Canada (NSERC) Postdoctoral Fellowship. The second author would like to acknowledge the support of the NSERC for this research under Research Grant Number RG-PIN 238298. Both authors would like to acknowledge the support of the InfoNet Media Centre funded by the Canadian Foundation for Innovation (CFI) under grant number CFI-3648.

Citation

Tsang, H.H. and Wiese, K.C. (2015), "A study of different annealing schedules in SARNA-predict: A permutation based SA algorithm for RNA folding", International Journal of Intelligent Computing and Cybernetics, Vol. 8 No. 2, pp. 152-171. https://doi.org/10.1108/IJICC-02-2015-0007

Publisher

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Emerald Group Publishing Limited

Copyright © 2015, Emerald Group Publishing Limited