Particle swarm optimization for finding RNA secondary structures

Purpose – The purpose of this paper is to present a new particle swarm optimization (PSO) algorithm called HelixPSO for finding ribonucleic acid (RNA) secondary structures that have a low energy and are similar to the native structure.Design/methodology/approach – Two variants of HelixPSO are described and compared to the recent algorithms Rna‐Predict, SARNA‐Predict, SetPSO and RNAfold. Furthermore, a parallel version of the HelixPSO is proposed.Findings – For a set of standard RNA test sequences it is shown experimentally that HelixPSO obtains a better average sensitivity than SARNA‐Predict and SetPSO and is as good as RNA‐Predict and RNAfold. When best values for different measures (e.g. number of correctly predicted base pairs, false positives and sensitivity) over several runs are compared, HelixPSO performs better than RNAfold, similar to RNA‐Predict, and is outperformed by SARNA‐Predict. It is shown that HelixPSO complements RNA‐Predict and SARNA‐Predict well since the algorithms show often very dif...

[1]  Jin Chu Wu,et al.  The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation , 2001, Bioinform..

[2]  D. Turner,et al.  Measuring the thermodynamics of RNA secondary structure formation. , 1997, Biopolymers.

[3]  D. Turner,et al.  Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. , 1998, Biochemistry.

[4]  Kay C Wiese,et al.  RnaPredict—An Evolutionary Algorithm for RNA Secondary Structure Prediction , 2008, TCBB.

[5]  Andries Petrus Engelbrecht,et al.  Determining RNA Secondary Structure using Set-based Particle Swarm Optimization , 2006, 2006 IEEE International Conference on Evolutionary Computation.

[6]  J. Sabina,et al.  Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.

[7]  L. D. Whitley,et al.  The Traveling Salesman and Sequence Scheduling : , 1990 .

[8]  B. Ganem.  RNA world , 1987, Nature.

[9]  Kay C. Wiese,et al.  Permutation-based RNA secondary structure prediction via a genetic algorithm , 2003, The 2003 Congress on Evolutionary Computation, 2003. CEC '03..

[10]  B J Fregly,et al.  Parallel global optimization with the particle swarm algorithm , 2004, International journal for numerical methods in engineering.

[11]  Jaroslaw Sobieszczanski-Sobieski,et al.  A Parallel Particle Swarm Optimization Algorithm Accelerated by Asynchronous Evaluations , 2005 .

[12]  G Benedetti,et al.  A genetic algorithm to search for optimal and suboptimal RNA secondary structures. , 1995, Biophysical chemistry.

[13]  C. Pleij,et al.  Dynamic competition between alternative structures in viroid RNAs simulated by an RNA folding algorithm. , 1998, Journal of molecular biology.

[14]  D. Mills,et al.  Q beta RNA bacteriophage: mapping cis-acting elements within an RNA genome , 1990, Journal of virology.

[15]  Herbert H. Tsang,et al.  SARNA-Predict: A Study of RNA Secondary Structure Prediction Using Different Annealing Schedules , 2007, 2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology.

[16]  Andrew Hendriks,et al.  Algorithms for RNA folding: a comparison of dynamic programming and parallel evolutionary algorithms , 2005, 2005 IEEE Congress on Evolutionary Computation.

[17]  James Kennedy,et al.  Particle swarm optimization , 1995, Proceedings of ICNN'95 - International Conference on Neural Networks.

[18]  Jan van Duin,et al.  Control of prokaryotic translational initiation by mRNA secondary structure , 1990 .

[19]  D. Turner,et al.  Predicting thermodynamic properties of RNA. , 1995, Methods in enzymology.

[20]  D. J. Smith,et al.  A Study of Permutation Crossover Operators on the Traveling Salesman Problem , 1987, ICGA.

[21]  Y. Rahmat-Samii,et al.  Parallel particle swarm optimization and finite- difference time-domain (PSO/FDTD) algorithm for multiband and wide-band patch antenna designs , 2005, IEEE Transactions on Antennas and Propagation.

[22]  K. Wiese,et al.  A permutation-based genetic algorithm for the RNA folding problem: a critical look at selection strategies, crossover operators, and representation issues. , 2003, Bio Systems.

[23]  Herbert H. Tsang,et al.  The significance of thermodynamic models in the accuracy improvement of RNA secondary structure prediction using permutation-based simulated annealing , 2007, 2007 IEEE Congress on Evolutionary Computation.

[24]  A. E. Walter,et al.  Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[25]  E. Siggia,et al.  Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[26]  D. E. Goldberg,et al.  Genetic Algorithm in Search , 1989 .

[27]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[28]  Andries Petrus Engelbrecht,et al.  Fundamentals of Computational Swarm Intelligence , 2005 .

[29]  Martin Middendorf,et al.  A Particle Swarm Optimizer for Finding Minimum Free Energy RNA Secondary Structures , 2007, 2007 IEEE Swarm Intelligence Symposium.

[30]  Greg Burns,et al.  LAM: An Open Cluster Environment for MPI , 2002 .

[31]  C. Pleij,et al.  The computer simulation of RNA folding pathways using a genetic algorithm. , 1995, Journal of molecular biology.

[32]  Mauro Birattari,et al.  How to assess and report the performance of a stochastic algorithm on a benchmark problem: mean or best result on a number of runs? , 2007, Optim. Lett..

[33]  C. Pleij,et al.  An APL-programmed genetic algorithm for the prediction of RNA secondary structure. , 1995, Journal of theoretical biology.

[34]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[35]  Bruce A. Shapiro,et al.  A massively parallel genetic algorithm for RNA secondary structure prediction , 1994, The Journal of Supercomputing.

[36]  L. Darrell Whitley,et al.  A Comparison of Genetic Sequencing Operators , 1991, ICGA.

[37]  Einar Andreas Rødland.  Pseudoknots in RNA Secondary Structures: Representation, Enumeration, and Prevalence , 2006, J. Comput. Biol..

[38]  D. Sankoff,et al.  RNA secondary structures and their prediction , 1984 .

[39]  Herbert H. Tsang,et al.  SARNA-Predict: A Simulated Annealing Algorithm for RNA Secondary Structure Prediction , 2006, 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology.

[40]  David E. Goldberg,et al.  AllelesLociand the Traveling Salesman Problem , 1985, ICGA.

[41]  Peter F. Stadler,et al.  Memory Efficient Folding Algorithms for Circular RNA Secondary Structures , 2006, German Conference on Bioinformatics.

[42]  Jürgen Branke,et al.  Multi-objective particle swarm optimization on computer grids , 2007, GECCO '07.

[43]  S. Le,et al.  Prediction of common secondary structures of RNAs: a genetic algorithm approach. , 2000, Nucleic acids research.

[44]  Scott D. Goodwin,et al.  Keep–Best Reproduction: A Local Family Competition Selection Strategy and the Environment it Flourishes in , 2001, Constraints.

[45]  Vladimir A. Ivanisenko,et al.  A fast genetic algorithm for RNA secondary structure analysis , 2002 .

[46]  Andrew Hendriks,et al.  Comparison of P-RnaPredict and mfold - algorithms for RNA secondary structure prediction , 2006, Bioinform..

[47]  Nan Yu,et al.  The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs , 2002, BMC Bioinformatics.

[48]  Jin Chu Wu,et al.  An annealing mutation operator in the genetic algorithms for RNA folding , 1996, Comput. Appl. Biosci..

[49]  J. Doudna.  Structural genomics of RNA , 2000, Nature Structural Biology.

[50]  Enrique Alba,et al.  Parallel Metaheuristics: A New Class of Algorithms , 2005 .

[51]  Ziya Arnavut,et al.  Fault diagnosis for airplane engines using Bayesian networks and distributed particle swarm optimization , 2007, Parallel Comput..