吉林大学学报(工学版) ›› 2010, Vol. 40 ›› Issue (增刊): 324-0327.

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Application of Markov chain in RNA secondary structure prediction

DONG Hao1, LIU Yuan-ning1, ZHANG Hao1, LI Zhi2   

  1. 1.College of Computer Science and Technology, Jilin University, Changchun 132012,China|2.College of Applied Technique, Changchun University of Science and Technology,Changchun 130022,China
  • Received:2010-03-06 Online:2010-09-01 Published:2010-09-01

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Abstract:

Based on Markov chain，a new method was proposed to predict the RNA secondary structure.Firstly，prefix and suffix matching algorithms were applied to find all the possible (including the pseudoknot) stem zones quickly, then free energy of stemloop stems was calculated, and finally RNAML was established to find the secondary structure with the minimum free energy. The experimental results show that proposed method reduces the computational complexity and improves specificity and sensitivity of prediction with high accuracy, so can predict pseudoknot structure.

Key words: computer application, bioinformatics, RNA secondary structure, free energy, Pseudo-knot, Markov chain

CLC Number: 

  • TP399
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