Title :
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
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;
Conference_Titel :
Evolutionary Computation, 2005. The 2005 IEEE Congress on
Conference_Location :
Edinburgh, Scotland
Print_ISBN :
0-7803-9363-5
DOI :
10.1109/CEC.2005.1554721
