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A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms

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Algorithms in Bioinformatics (WABI 2011)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 6833))

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Abstract

We extend an hypergraph representation, introduced by Finkelstein and Roytberg, to unify dynamic programming algorithms in the context of RNA folding with pseudoknots. Classic applications of RNA dynamic programming (Energy minimization, partition function, base-pair probabilities…) are reformulated within this framework, giving rise to very simple algorithms. This reformulation allows one to conceptually detach the conformation space/energy model – captured by the hypergraph model – from the specific application, assuming unambiguity of the decomposition. To ensure the latter property, we propose a new combinatorial methodology based on generating functions. We extend the set of generic applications by proposing an exact algorithm for extracting generalized moments in weighted distribution, generalizing a prior contribution by Miklos and al. Finally, we illustrate our full-fledged programme on three exemplary conformation spaces (secondary structures, Akutsu’s simple type pseudoknots and kissing hairpins). This readily gives sets of algorithms that are either novel or have complexity comparable to classic implementations for minimization and Boltzmann ensemble applications of dynamic programming.

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Author information

Authors and Affiliations

  1. LIX, École Polytechnique/CNRS/INRIA AMIB, France

    Yann Ponty

  2. LRI, Université Paris-Sud/XI/INRIA AMIB, France

    Cédric Saule

  3. Institute for Research in Immunology and Cancer, Montreal, Quebec, Canada

    Cédric Saule

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  1. Yann Ponty
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  2. Cédric Saule
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Editors and Affiliations

  1. National Center for Biotechnology Information, U.S. National Library of Medicine, 8600 Rockville Pike, 20894, Bethesda, MD, USA

    Teresa M. Przytycka

  2. Institut National de Recherche en Informatique et en Automatique (INRIA) and Université Lyon 1 (UCBL), 43 bd du 11 Novembre 1918, 69622, Villeurbanne cedex, France

    Marie-France Sagot

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Ponty, Y., Saule, C. (2011). A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms. In: Przytycka, T.M., Sagot, MF. (eds) Algorithms in Bioinformatics. WABI 2011. Lecture Notes in Computer Science(), vol 6833. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-23038-7_22

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  • DOI: https://doi.org/10.1007/978-3-642-23038-7_22

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