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Annual Symposium on Combinatorial Pattern Matching

CPM 2000: Combinatorial Pattern Matching pp 33–45Cite as

Some Results on Flexible-Pattern Discovery

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Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1848))

Abstract

Given an input sequence of data, a “rigid” pattern is a repeating sequence, possibly interspersed with “dont care” characters. In practice, the patterns or motifs of interest are the ones that also allow a variable number of gaps (or “dont care” characters): we call these the flexible motifs. The number of rigid motifs could potentially be exponential in the size of the input sequence and in the case where the input is a sequence of real numbers, there could be uncountably infinite number of motifs (assuming two real numbers are equal if they are within some δ > 0 of each other). It has been shown earlier that by suitably defining the notion of maximality and redundancy, there exists only a linear (or no more than 3n) number of irredundant motifs and a polynomial time algorithm to detect these irredundant motifs. Here we present a uniform framework that encompasses both rigid and flexible motifs with generalizations to sequence of sets and real numbers and show a somewhat surprising result that the number of irredundant flexible motifs still have a linear bound. However, the algorithm to detect them has a higher complexity than that of the rigid motifs.

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Author information

Authors and Affiliations

  1. Bioinformatics and Pattern Discovery, IBM Thomas J. Watson Research Center, Yorktown Heights, NY, 10598, USA

    Laxmi Parida

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  1. Laxmi Parida
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Editors and Affiliations

  1. Dipartimento di Matematica ed Applicazioni, Universitá die Palermo, Via Archirafi 34, 90123, Palermo, Italy

    Raffaele Giancarlo

  2. Centre de recherches mathématiques, Université de Montréal, CP 6128, succursale Centre-Ville, Montréal, Québec, Canada, H3C 3J7

    David Sankoff

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© 2000 Springer-Verlag Berlin Heidelberg

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Parida, L. (2000). Some Results on Flexible-Pattern Discovery. In: Giancarlo, R., Sankoff, D. (eds) Combinatorial Pattern Matching. CPM 2000. Lecture Notes in Computer Science, vol 1848. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45123-4_5

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  • DOI: https://doi.org/10.1007/3-540-45123-4_5

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-67633-1

  • Online ISBN: 978-3-540-45123-5

  • eBook Packages: Springer Book Archive

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