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Computing all suboptimal alignments in linear space

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Combinatorial Pattern Matching (CPM 1994)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 807))

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Abstract

Recently, a new compact representation for suboptimal alignments was proposed by Naor and Brutlag (1993). The kernel of that representation is a minimal directed acyclic graph (DAG) containing all suboptimal alignments. In this paper, we propose a method that computes such a DAG in space linear to the graph size. Let F be the area of the region of the dynamicprogramming matrix bounded by the suboptimal alignments and W the maximum width of that region. For two sequences of lengths M and N, it is shown that the worst-case running time is O(MN+F log log W). To exploit the computed DAG, we employ a variant of Aho-Corasick pattern matching machine (Aho and Corasick, 1975) to locate all occurrences of specified patterns, and then find a path in the DAG that maximizes the sum of the scores of the non-overlapping patterns occurring in it. An example illustrates the utility.

This work was supported by grant RO1 LM05110 from the National Library of Medicine.

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Authors and Affiliations

  1. Department of Computer Science and Engineering, The Pennsylvania State University, 16802, University Park, PA, USA

    Kun -Mao Chao

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  1. Kun -Mao Chao
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Maxime Crochemore Dan Gusfield

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© 1994 Springer-Verlag Berlin Heidelberg

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Chao, K.M. (1994). Computing all suboptimal alignments in linear space. In: Crochemore, M., Gusfield, D. (eds) Combinatorial Pattern Matching. CPM 1994. Lecture Notes in Computer Science, vol 807. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-58094-8_3

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  • DOI: https://doi.org/10.1007/3-540-58094-8_3

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-58094-2

  • Online ISBN: 978-3-540-48450-9

  • eBook Packages: Springer Book Archive

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