吉林大学学报(工学版) ›› 2011, Vol. 41 ›› Issue (增刊2): 250-253.

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RNA second structure comparison based on dynamic programming

LI Zhi1,2, LIU Yuan-ning2, ZHANG Hao2, SHEN Ting-jie2, LI Jie2, ZHAI Hong-liang2   

  1. 1. College of computer Science and Technology, Changchun University of Science and Technology, Changchun 130022, China;
    2. College of computer Science and Technology, Jilin University, Changchun 130012, China
  • Received:2011-03-06 Online:2011-09-30 Published:2011-09-30

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Abstract:

Traditional description methods of RNA secondary structure could lead higher complexity of time in RNA structure comparison.This article offers a vector method of describing RNA secondary structure.Then,we compare RNA secondary structures tree by dynamic programming and those structures come from NA segments of highly pathogenic H5N1 virus.It is superior to the method of minimum free energy on time complexity.And it shows RNAs hold higher similar structure when they hold stronger pathogenicity,which could be a good guide for biological experiments.

Key words: bioinformatics, RNA secondary structure, vector tree, H5N1, dynamic programming

CLC Number: 

  • TP399


[1] Jin E Y,Qin J,Reidys C M.combinatorics of RNAs tructures with pseudoknots
[J].Bulletion of Math-e matical Biology,2008,70(1):45-67.

[2] Needleman S B,Wunsch C D.A general method applicable to the search for similarities in the aminoa cid sequence of two proteins
[J].JMB,1970,48 (3):443-453.

[3] Wu Chan-shuo,Huang Guan-sheng.A practical edit-distance model for RNA secondary-structure comparison
[C]∥2009Ninth IEEE International Conference on Bioinformatics and Bioengineering.Taichung TAIWAN,2009:176-183

[4] Shapiro B,Zhang K.comparing multiple secondarys tructures using tree comparesons
[J].comp.Appl.B iosci.1990,4(6):309-318.

[5] Julien Allali,Marie-France Sagot.A new distance for high level RNA secondary structure comparison
[J].IEEE/ACM Transactions on computational Biology and Bioinformatics,2005,1(2):3-14.
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