Abstract
Interaction between two RNA molecules plays a crucial role in many medical and biological processes such as gene expression regulation. In this process, an RNA molecule prohibits the translation of another RNA molecule by establishing stable interactions with it. Some algorithms have been formed to predict the structure of the RNA–RNA interaction. High computational time is a common challenge in most of the presented algorithms. In this context, a heuristic method is introduced to accurately predict the interaction between two RNAs based on minimum free energy (MFE). This algorithm uses a few dot matrices for finding the secondary structure of each RNA and binding sites between two RNAs. Furthermore, a parallel version of this method is presented. We describe the algorithm’s concurrency and parallelism for a multicore chip. The proposed algorithm has been performed on some datasets including CopA-CopT, R1inv-R2inv, Tar-Tar*, DIS-DIS, and IncRNA54-RepZ in Escherichia coli bacteria. The method has high validity and efficiency, and it is run in low computational time in comparison to other approaches.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Huang FWD, Qin J, Reidys CM et al (2010) Target prediction and a statistical sampling algorithm for RNA-RNA interaction. Bioinformatics 26:175–181
Salari R, Backofen R, Sahinalp SC (2010) Fast prediction of RNA-RNA interaction. Algorithms Mol Biol 5:5–15
Tafer H, Hofacker IL (2008) RNAplex: a fast tool for RNA-RNA interaction search. Bioinformatics 24:2657–2663
Mneimneh S (2009) On the approximation of optimal structures for RNA-RNA interaction. Trans Comput Biol Bioinform 6:682–688
Andronescu M, Zhang ZC, Condon A (2005) Secondary structure prediction of interacting RNA molecules. J Mol Biol 345:987–1001
Bernhart S, Tafer H, Mückstein U et al (2006) Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol Biol 1–3
Dirks R, Bios J, Schaeffer JM et al (2007) Thermodynamic analysis of interacting nucleic acid strands. Soc Ind Appl Math 49:65–88
Rehmsmeier M, Steffen P, Hochsmann M et al (2004) Fast and effective prediction of microRNA/target duplexes. RNA 10:1507–1517
Markham NR, Zuker M (2008) UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol 453:3–31
Alkan C, Karakoc E, Nadeau JH et al (2006) RNA-RNA interaction prediction and antisense RNA target search. J. Comput Biol 13:267–282
Mückstein U, Tafer H, Bernhart S et al (2009) Translational control by RNA-RNA interaction: Improved computation of RNA-RNA binding thermodynamics. Bioinform Res Dev 13:114–127
Mückstein U, Tafer H, Hackermuller J et al (2006) Thermodynamics of RNA-RNA binding. Bioinformatics 22:1177–1182
Busch A, Richter AS, Backofen R (2008) IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions. Bioinformatics 24:2849–2856
Kato Y, Akutsu T, Seki H (2009) A grammatical approach to RNA-RNA interaction prediction. Pattern Recogn 42:531–538
Aksay C, Karakoc E, Kin Ho C et al. (2007) ncRNA discovery and functional identification via sequence motifs. Technical Report TR 1–9
Selim GA (1989) The design and analysis of parallel algorithms. ISBN 0-33-23005b-3
Seemann SE, Richter AS, Gesell T et al (2011) PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences. Bioinformatics 2:211–219
Chitsaz H, Salari R, Sahinalp SC et al (2009) A partition function algorithm for interacting nucleic acid strands. Bioinformatics 25:i365–i373
Li AX, Marz M, Qin J et al (2011) RNA–RNA interaction prediction based on multiple sequence alignments. Bioinformatics 4:456–463
Acknowledgements
Special thanks to Professor Fatemeh Zare-Mirakabad and Nasrollah Moghadam-charkari for their valuable consultancy in improving this work.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Montaseri, S. (2015). Fast Prediction of RNA–RNA Interaction Using Heuristic Algorithm. In: Picardi, E. (eds) RNA Bioinformatics. Methods in Molecular Biology, vol 1269. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2291-8_7
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2291-8_7
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2290-1
Online ISBN: 978-1-4939-2291-8
eBook Packages: Springer Protocols