吉林大学学报(工学版) ›› 2015, Vol. 45 ›› Issue (2): 613-618.doi: 10.13229/j.cnki.jdxbgxb201502041

• Orignal Article • Previous Articles     Next Articles

RNA pseudoknot prediction based on local structure interaction

LIU Yuan-ning1,2, AI Lu-lu1,2,DUAN Yun-na1,2,LI Zhi3,TIAN Ming-yao4,ZHANG Hao1,2   

  1. 1.College of Computer Science and Technology, Jilin University, Changchun 130012, China;
    2.Symbol Computation and Knowledge Engineering of Ministry of Education,Jilin University,Changchun 130012,China;
    3.College of Applied Technique, Changchun University of Science and Technology, Changchun 130022, China;
    4.Military Veterinary Institute, Academy of Military Medical Science, Changchun 130122,China
  • Received:2013-05-19 Online:2015-04-01 Published:2015-04-01

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Abstract: According to the interaction between local structures of RNA, a new algorithm, named LIFold, is presented to predict RNA secondary structure with pseudoknot. For a given RNA sequence, first, the optimal RNA secondary structure without pseudoknot is generated based on the method of free energy calculation. Then, the pseudoknot stems are obtained using local structure pairing interaction, and an energy calculation model with pseudoknot is established on the basis of the optimal structure. Finally, the RNA secondary structure with pseudoknot is obtained using optimization algorithm. Using the test data of HotKnots, the sensitivity and Positive Predict Value (PPV) reach 84% and 80% respectively. Using the test data based on PseudoBase database, the sensitivity and PPV reach 78% and 73% respectively. Comparing to HotKnots, ILM, PknotsRG IPknot and FlexStem softwares, the accuracy of the proposed algorithm, LIfold, is higher.

Key words: computer application, RNA secondary structure, pseudoknot, minimal free energy, pairing interaction

CLC Number: 

  • TP399
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