A genetic algorithm for predicting RNA pseudoknot structures

Authors:
Dongkyu Lee;Kyungsook Han
Affiliations:
School of Computer Science and Engineering, Inha University, Inchon, Korea;School of Computer Science and Engineering, Inha University, Inchon, Korea
Venue:
ICCS'03 Proceedings of the 2003 international conference on Computational science: PartIII
Year:
2003

Citing 2
Cited 0

A massively parallel genetic algorithm for RNA secondary structure prediction

The Journal of Supercomputing
Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots

Discrete Applied Mathematics - Special volume on combinatorial molecular biology

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Abstract

An RNA pseudoknot is a tertiary structure element formed when bases of a single-stranded loop pair with complementary bases outside the loop. Computational determination of the RNA folding structure with pseudoknots from the linear sequence is a complex problem involving both spatial reasoning and the use of knowledge of chemistry and biology. We have developed a genetic algorithm for predicting the RNA folding structure with pseudoknots of any type. This paper analyzes the predictions by the genetic algorithm with different population generation methods and fitness functions, and compares the predictions to those by a dynamic programming method.