Fast Prediction of RNA-RNA Interaction

  • Raheleh Salari
  • Rolf Backofen
  • S. Cenk Sahinalp
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5724)


Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting the translation of an mRNA by establishing stable interactions with a target sequence. There is great demand for efficient computational methods to predict the specific interaction between an ncRNA and its target mRNA(s). There are a number of algorithms in the literature which can predict a variety of such interactions - unfortunately at a very high computational cost. Although some existing target prediction approaches are much faster, they are specialized for interactions with a single binding site.

In this paper we present a novel algorithm to accurately predict the minimum free energy structure of RNA-RNA interaction under the most general type of interactions studied in the literature. Moreover, we introduce a fast heuristic method to predict the specific (multiple) binding sites of two interacting RNAs. We verify the performance of our algorithms for joint structure and binding site prediction on a set of known interacting RNA pairs. Experimental results show our algorithms are highly accurate and outperform all competitive approaches.




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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Raheleh Salari
    • 1
  • Rolf Backofen
    • 2
  • S. Cenk Sahinalp
    • 1
  1. 1.School of Computing ScienceSimon Fraser UniversityBurnabyCanada
  2. 2.Bioinformatics GroupAlbert-Ludwigs-UniversityFreiburgGermany

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