Algorithms for RNA folding: a comparison of dynamic programming and parallel evolutionary algorithms

Author

Wiese, Kay C. ; Hendriks, Andrew ; Poonian, Jagdeep

Author_Institution

Sch. of Comput. Sci., Simon Fraser Univ., Surrey, BC

Volume

1

fYear

2005

fDate

5-5 Sept. 2005

Firstpage

475

Abstract

This paper presents a comparison of two types of algorithms for RNA secondary structure prediction: an implementation of Nussinov´s dynamic programming algorithm (DPA), and P-RnaPredict, a parallel evolutionary algorithm (EA). The research presented here builds on previous work and examines the results from tests of three RNA sequences that are 118, 543, and 784 nucleotides in length. A variety of EA parameter settings were employed based on previous experimentation. Predicted structures were compared to those generated by the Nussinov DPA and to known structures to determine relative accuracy. Results indicate that the EA demonstrated high prediction accuracy and outperformed the Nussinov DPA on all tested sequences

Keywords

biology computing; dynamic programming; evolutionary computation; macromolecules; parallel algorithms; Nussinov dynamic programming algorithm; P-RnaPredict; RNA folding algorithm; RNA secondary structure prediction; RNA sequence; parallel evolutionary algorithm; Accuracy; Concurrent computing; Convergence; Dynamic programming; Evolutionary computation; Heuristic algorithms; Predictive models; Proteins; RNA; Thermodynamics;

fLanguage

English

Publisher

ieee

Conference_Titel

Evolutionary Computation, 2005. The 2005 IEEE Congress on

Conference_Location

Edinburgh, Scotland

Print_ISBN

0-7803-9363-5

Type

conf

DOI

10.1109/CEC.2005.1554721

Filename

1554721