RactIP: Fast and accurate prediction of RNA-RNA interaction using integer programming

Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu

Research output: Contribution to journalArticle

42 Citations (Scopus)

Abstract

Motivation: Considerable attention has been focused on predicting RNA-RNA interaction since it is a key to identifying possible targets of non-coding small RNAs that regulate gene expression posttranscriptionally. A number of computational studies have so far been devoted to predicting joint secondary structures or binding sites under a specific class of interactions. In general, there is a tradeoff between range of interaction type and efficiency of a prediction algorithm, and thus efficient computational methods for predicting comprehensive type of interaction are still awaited. Results: We present RactIP, a fast and accurate prediction method for RNA-RNA interaction of general type using integer programming. RactIP can integrate approximate information on an ensemble of equilibrium joint structures into the objective function of integer programming using posterior internal and external base-paring probabilities. Experimental results on real interaction data show that prediction accuracy of RactIP is at least comparable to that of several state-of-the-art methods for RNA-RNA interaction prediction. Moreover, we demonstrate that RactIP can run incomparably faster than competitive methods for predicting joint secondary structures.

Original languageEnglish
Pages (from-to)i460-i466
JournalBioinformatics
Volume27
Issue number13
DOIs
Publication statusPublished - 2011
Externally publishedYes

Fingerprint

Integer programming
Integer Programming
RNA
Prediction
Interaction
Joints
Secondary Structure
Small Untranslated RNA
Computational methods
Gene expression
Binding sites
Computational Methods
Gene Expression
Binding Sites
Ensemble
Objective function
Trade-offs
Integrate
Internal
Target

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Medicine(all)
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

RactIP : Fast and accurate prediction of RNA-RNA interaction using integer programming. / Kato, Yuki; Sato, Kengo; Hamada, Michiaki; Watanabe, Yoshihide; Asai, Kiyoshi; Akutsu, Tatsuya.

In: Bioinformatics, Vol. 27, No. 13, 2011, p. i460-i466.

Research output: Contribution to journalArticle

Kato, Yuki ; Sato, Kengo ; Hamada, Michiaki ; Watanabe, Yoshihide ; Asai, Kiyoshi ; Akutsu, Tatsuya. / RactIP : Fast and accurate prediction of RNA-RNA interaction using integer programming. In: Bioinformatics. 2011 ; Vol. 27, No. 13. pp. i460-i466.
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