吉林大学学报(工学版) ›› 2011, Vol. 41 ›› Issue (02): 452-0457.

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Prediction of RNA secondary structure using dynamic programming algorithm based on stems

YU Jun1,2, ZHANG Chang-hai1,2, ZHANG Hao1,2, ZHAO Guan-nan1,2, LIU Yuan-ning1,2   

  1. 1.College of Computer Science and Technology, Jilin University, Changchun 130012, China;2.Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
  • Received:2010-08-21 Published:2011-03-01

Abstract:

In this paper, a new method is presented to predict the RNA secondary structure, which combines the characteristics and advantages of combinatorial optimization approach and traditional dynamic programming algorithm. First, for a given RNA sequence, the set containing all possible stems is obtained. Then, adopting what are called loop dependent energy rules, the secondary structure is constructed using dynamic programming algorithm based on stems. The proposed program was tested by the case with RNA sequences. Experiment results show that the proposed program is better than genetic algorithm in terms of specificity, sensitivity and Matthews correlation coefficient, and the complexity of the program is lower than that of traditional dynamic programming algorithm.

Key words: computer application, bioinformatics, ribonucleic acid(RNA), secondary structure, stems, dynamic programming algorithm

CLC Number: 

  • TP301
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