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Annual Symposium on Combinatorial Pattern Matching

CPM 2012: Combinatorial Pattern Matching pp 306–320Cite as

Local Exact Pattern Matching for Non-fixed RNA Structures

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7354))

Abstract

Detecting local common sequence-structure regions of RNAs is a biologically meaningful problem. By detecting such regions, biologists are able to identify functional similarity between the inspected molecules. We developed dynamic programming algorithms for finding common structure-sequence patterns between two RNAs. The RNAs are given by their sequence and a set of potential base pairs with associated probabilities. In contrast to prior work which matches fixed structures, we support the arc breaking edit operation; this allows to match only a subset of the given base pairs. We present an O(n 3) algorithm for local exact pattern matching between two nested RNAs, and an O(n 3logn) algorithm for one nested RNA and one bounded-unlimited RNA.

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of Haifa, Mount Carmel, Haifa, Israel

    Mika Amit & Gad M. Landau

  2. Department of Computer Science and Engineering, NYU-Poly, Brooklyn, NY, USA

    Gad M. Landau

  3. Bioinformatics, Institute of Computer Science, Albert-Ludwigs-Universität, Freiburg, Germany

    Rolf Backofen, Steffen Heyne, Mathias Möhl, Christina Schmiedl & Sebastian Will

  4. Center for Biological Signaling Studies (BIOSS), Albert-Ludwigs-Universität, Freiburg, Germany

    Rolf Backofen

  5. CSAIL and Mathematics Department, MIT, Cambridge, MA, USA

    Sebastian Will

Authors
  1. Mika Amit
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  2. Rolf Backofen
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  3. Steffen Heyne
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  4. Gad M. Landau
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  5. Mathias Möhl
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  6. Christina Schmiedl
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  7. Sebastian Will
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Editor information

Editors and Affiliations

  1. Department of Computer Science, University of Helsinki, Gustaf Hällström Katu 2b, P.O. Box 68, 00014, Helsinki, Finland

    Juha Kärkkäinen

  2. Faculty of Technology, University of Bielefeld, Universitätsstraße 25, 33615, Bielefeld, Germany

    Jens Stoye

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Amit, M. et al. (2012). Local Exact Pattern Matching for Non-fixed RNA Structures. In: Kärkkäinen, J., Stoye, J. (eds) Combinatorial Pattern Matching. CPM 2012. Lecture Notes in Computer Science, vol 7354. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31265-6_25

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  • DOI: https://doi.org/10.1007/978-3-642-31265-6_25

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-31264-9

  • Online ISBN: 978-3-642-31265-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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