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biRNA: Fast RNA-RNA Binding Sites Prediction

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Algorithms in Bioinformatics (WABI 2009)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5724))

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Abstract

We present biRNA, a novel algorithm for prediction of binding sites between two RNAs based on minimization of binding free energy. Similar to RNAup approach [30], we assume the binding free energy is the sum of accessibility and the interaction free energies. Our algorithm maintains tractability and speed and also has two important advantages over previous similar approaches: (1) biRNA is able to predict multiple simultaneous binding sites and (2) it computes a more accurate interaction free energy by considering both intramolecular and intermolecular base pairing. Moreover, biRNA can handle crossing interactions as well as hairpins interacting in a zigzag fashion. To deal with simultaneous accessibility of binding sites, our algorithm models their joint probability of being unpaired. Since computing the exact joint probability distribution is intractable, we approximate the joint probability by a polynomially representable graphical model namely a Chow-Liu tree-structured Markov Random Field. Experimental results show that biRNA outperforms RNAup and also support the accuracy of our approach. Our proposed Bayesian approximation of the Boltzmann joint probability distribution provides a powerful, novel framework that can also be utilized in other applications.

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Author information

Authors and Affiliations

  1. School of Computing Science, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, Canada

    Hamidreza Chitsaz & S. Cenk Sahinalp

  2. Institut für Informatik, Albert-Ludwigs-Universität, Georges-Koehler-Allee, Freiburg, Germany

    Rolf Backofen

Authors
  1. Hamidreza Chitsaz
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  2. Rolf Backofen
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  3. S. Cenk Sahinalp
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Editor information

Editors and Affiliations

  1. Center for Bioinformatics and Computational Biology, and Department of Computer Science, University of Maryland, MD, College Park, USA

    Steven L. Salzberg

  2. Department of Computer Sciences, The University of Texas at Austin, TX, USA

    Tandy Warnow

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© 2009 Springer-Verlag Berlin Heidelberg

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Chitsaz, H., Backofen, R., Sahinalp, S.C. (2009). biRNA: Fast RNA-RNA Binding Sites Prediction. In: Salzberg, S.L., Warnow, T. (eds) Algorithms in Bioinformatics. WABI 2009. Lecture Notes in Computer Science(), vol 5724. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04241-6_3

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  • DOI: https://doi.org/10.1007/978-3-642-04241-6_3

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-04240-9

  • Online ISBN: 978-3-642-04241-6

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