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An algorithm for locating non-overlapping regions of maximum alignment score

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Combinatorial Pattern Matching (CPM 1993)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 684))

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Abstract

In this paper we present an O(N 2log2 N) algorithm for finding the two non-overlapping substrings of a given string of length N which have the highest-scoring alignment between them. This significantly improves the previously best known bound of O(N 3) for the worst-case complexity of this problem. One of the central ideas in the design of this algorithm is that of partitioning a matrix into pieces in such a way that all submatrices of interest for this problem can be put together as the union of very few of these pieces. Other ideas include the use of candidate-lists, an application of the ideas of Apostolico et al. [1] to our problem domain, and divide and conquer techniques.

Supported in part by NSF grant CCR-9108969.

Supported in part by NLM grant LM-04960 and NSF grant CCR-9002351.

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References

  1. A. Apostolico, M.J. Atallah, L.L. Larmore, and S. McFaddin, “Efficient Parallel Algorithms for String Editing and Related Problems,” SIAM J. Comput. 19 (1990), 968–988.

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Authors and Affiliations

  1. Department of Computer Science, University of Arizona, 85721, Tucson, AZ

    Sampath K. Kannan & Eugene. W. Myers

Authors
  1. Sampath K. Kannan
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  2. Eugene. W. Myers
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Editor information

Alberto Apostolico Maxime Crochemore Zvi Galil Udi Manber

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© 1993 Springer-Verlag Berlin Heidelberg

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Kannan, S.K., Myers, E.W. (1993). An algorithm for locating non-overlapping regions of maximum alignment score. In: Apostolico, A., Crochemore, M., Galil, Z., Manber, U. (eds) Combinatorial Pattern Matching. CPM 1993. Lecture Notes in Computer Science, vol 684. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0029798

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  • DOI: https://doi.org/10.1007/BFb0029798

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-56764-6

  • Online ISBN: 978-3-540-47732-7

  • eBook Packages: Springer Book Archive

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