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Algorithms for Forest Pattern Matching

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Combinatorial Pattern Matching (CPM 2010)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6129))

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Abstract

Ordered labelled trees are trees where the left-to-right order among siblings is significant. An ordered labelled forest is a sequence of ordered labelled trees. Given an ordered labelled forest F (“the target forest”) and an ordered labelled forest G (“the pattern forest”), the forest pattern matching problem is to find a sub-forest F′ of F such that F′ and G are the most similar over all possible F′. In this paper, we present efficient algorithms for the forest pattern matching problem for two types of sub-forests: closed subforests and closed substructures. As RNA molecules’ secondary structures could be represented as ordered labelled forests, our algorithms can be used to locate the structural or functional regions in RNA secondary structures.

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Author information

Authors and Affiliations

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

    Kaizhong Zhang & Yunkun Zhu

Authors
  1. Kaizhong Zhang
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  2. Yunkun Zhu
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Editor information

Editors and Affiliations

  1. Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA, and Bar-Ilan University, 52900, Ramat-Gan, Israel

    Amihood Amir

  2. IBM T.J. Watson Research Center, Yorktown Heights, NY, USA

    Laxmi Parida

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Zhang, K., Zhu, Y. (2010). Algorithms for Forest Pattern Matching. In: Amir, A., Parida, L. (eds) Combinatorial Pattern Matching. CPM 2010. Lecture Notes in Computer Science, vol 6129. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13509-5_1

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  • DOI: https://doi.org/10.1007/978-3-642-13509-5_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-13508-8

  • Online ISBN: 978-3-642-13509-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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