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Computing Similarity between RNA Structures

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Combinatorial Pattern Matching (CPM 1999)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1645))

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Abstract

The primary structure of a ribonucleic acid (RNA) molecule is a sequence of nucleotides (bases) over the alphabet {A;C;G;U}. The secondary or tertiary structure of an RNA is a set of base-pairs (nucleotide pairs) which forms bonds between A - U and C - G. For secondary structures, these bonds have been traditionally assumed to be one-to-one and non-crossing

This paper considers a notion of similarity between two RNA molecule structures taking into account the primary, the secondary and the tertiary structures. We show that in general this problem is NP-hard for tertiary structures. We present algorithms for the case where at least one of the RNA involved is of secondary structures. We then show that this algorithm might be used to deal with the practical application. We also show an approximation algorithm.

Research supported partially by the Natural Sciences and Engineering Research Council of Canada under Grant No. OGP0046373.

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Author information

Authors and Affiliations

  1. Dept. of Computer Science, University of Western Ontario, London, Ont. N6A 5B7, Canada

    Kaizhong Zhang

  2. Dept. of Computer Science, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong

    Lusheng Wang

  3. Dept. of Mathematics, Peking University, Beijing, 100871, P.R. China

    Bin Ma

Authors
  1. Kaizhong Zhang
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  2. Lusheng Wang
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  3. Bin Ma
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Editor information

Editors and Affiliations

  1. Institute Gaspard-Monge, University of Marne-la-Vallée, F 77454, Marne-la-Vallée Cedex 2, France

    Maxime Crochemore

  2. Department of Computer Science, University of Warwick, Coventry, CV4 7AL, England

    Mike Paterson

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© 1999 Springer-Verlag Berlin Heidelberg

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Zhang, K., Wang, L., Ma, B. (1999). Computing Similarity between RNA Structures. In: Crochemore, M., Paterson, M. (eds) Combinatorial Pattern Matching. CPM 1999. Lecture Notes in Computer Science, vol 1645. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-48452-3_21

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  • DOI: https://doi.org/10.1007/3-540-48452-3_21

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-66278-5

  • Online ISBN: 978-3-540-48452-3

  • eBook Packages: Springer Book Archive

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