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

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 post-transcriptionally. 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 trade-off 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. Availability: RactIP is implemented in C++, and the source code is available at http://www.ncrna.org/software/ractip/ Contact: ykato@kuicr.kyoto-u.ac.jp; satoken@k.u-tokyo.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.

[1]  H. Orland,et al.  Prediction of RNA secondary structures with pseudoknots , 2010 .

[2]  Rolf Backofen,et al.  Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding , 2010, RECOMB.

[3]  Christian M. Reidys,et al.  Target prediction and a statistical sampling algorithm for RNA–RNA interaction , 2009, Bioinform..

[4]  Tatsuya Akutsu,et al.  Dynamic Programming Algorithms for RNA Structure Prediction with Binding Sites , 2010, Pacific Symposium on Biocomputing.

[5]  Rolf Backofen,et al.  Fast prediction of RNA-RNA interaction , 2009, Algorithms for Molecular Biology.

[6]  Christian M. Reidys,et al.  Partition function and base pairing probabilities for RNA-RNA interaction prediction , 2009, Bioinform..

[7]  Hamidreza Chitsaz,et al.  A partition function algorithm for interacting nucleic acid strands , 2009, Bioinform..

[8]  Tatsuya Akutsu,et al.  A grammatical approach to RNA-RNA interaction prediction , 2009, Pattern Recognit..

[9]  Kiyoshi Asai,et al.  Prediction of RNA secondary structure using generalized centroid estimators , 2009, Bioinform..

[10]  Tatsuya Akutsu,et al.  Prediction of RNA secondary structure with pseudoknots using integer programming , 2009, BMC Bioinformatics.

[11]  Rolf Backofen,et al.  IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions , 2008, Bioinform..

[12]  Knut Reinert,et al.  Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization , 2007, BMC Bioinformatics.

[13]  J. Vogel,et al.  Target identification of small noncoding RNAs in bacteria. , 2007, Current opinion in microbiology.

[14]  Süleyman Cenk Sahinalp,et al.  taveRNA: a web suite for RNA algorithms and applications , 2007, Nucleic Acids Res..

[15]  Serafim Batzoglou,et al.  CONTRAfold: RNA secondary structure prediction without physics-based models , 2006, ISMB.

[16]  Peter F. Stadler,et al.  Partition function and base pairing probabilities of RNA heterodimers , 2006, Algorithms for Molecular Biology.

[17]  Kaizhong Zhang,et al.  RNA-RNA Interaction Prediction and Antisense RNA Target Search , 2006, J. Comput. Biol..

[18]  Peter F. Stadler,et al.  Thermodynamics of RNA-RNA Binding , 2006, German Conference on Bioinformatics.

[19]  A. Condon,et al.  Secondary structure prediction of interacting RNA molecules. , 2005, Journal of molecular biology.

[20]  R. Giegerich,et al.  Fast and effective prediction of microRNA/target duplexes. , 2004, RNA.

[21]  M. Zuker,et al.  Prediction of hybridization and melting for double-stranded nucleic acids. , 2004, Biophysical journal.

[22]  D. Pervouchine.  IRIS: intermolecular RNA interaction search. , 2004, Genome informatics. International Conference on Genome Informatics.

[23]  Ivo L. Hofacker,et al.  Vienna RNA secondary structure server , 2003, Nucleic Acids Res..

[24]  C. Ehresmann,et al.  RNA loop-loop interactions as dynamic functional motifs. , 2002, Biochimie.

[25]  S. Brantl,et al.  Antisense-RNA regulation and RNA interference. , 2002, Biochimica et biophysica acta.

[26]  Klas Flärdh,et al.  Antisense RNAs everywhere? , 2002, Trends in genetics : TIG.

[27]  S. Eddy.  Non–coding RNA genes and the modern RNA world , 2001, Nature Reviews Genetics.

[28]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .