吉林大学学报(工学版) ›› 2014, Vol. 44 ›› Issue (01): 191-195.doi: 10.13229/j.cnki.jdxbgxb201401032

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Selecting highly effective siRNAs by thermodynamics of siRNA-mRNA binding

LIU Yuan-ning1,2, XU Bao-lin1,2, ZHANG Hao1,2, CHEN Jing-bo1,2, HAN Ye1,2, YU Jian-long1   

  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
  • Received:2012-12-18 Online:2014-01-01 Published:2014-01-01

Abstract:

The thermodynamic of interactions between siRNAs and target mRNAs is crucial for the efficiency of its interference. RNAup is a software provided by Vienna RNA package, which can predict the accessibility of target region. By adding its predicted thermodynamic characteristics to the SiRNA sequence features and screening the efficient siRNA with support vector machines, the model can well predict efficient siRNA that the accuracy rate is up to 88.12%, the sensitivity and specificity are up to 88.35% and 87.94%, respectively.

Key words: computer application, thermodynamics, RNAi, SVM, prediction of siRNA functionality

CLC Number: 

  • TP399

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