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Erschienen in:
2014 | OriginalPaper | Buchkapitel
Prediction Nucleic Acid Secondary Structure with Planar Pseudoknots and Genetic Algorithm
verfasst von : Kai Zhang, Xinquan Huang, Wei Hu, Jun Liu
Erschienen in: Bio-Inspired Computing - Theories and Applications
Verlag: Springer Berlin Heidelberg
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In recent years, DNA and RNA molecules have shown great potential as a design medium for the construction of nanostructures and the programmed assembly of molecular computing. In this paper, we propose a novel genetic algorithm to predict nucleic acid secondary structure with planar pseudoknots. In our algorithm, the free energy and the number of continues base pairs stacking are used as fitness function to evaluate the individuals. We have compared the results obtained by our algorithm with RNAStructure. As will be discussed, our algorithm can efficiently predict the planar pseudoknots with lower free energy and more continues base pairs stacking.