Finding Optimal Pairs of Cooperative and Competing Patterns with Bounded Distance

  • Shunsuke Inenaga
  • Hideo Bannai
  • Heikki Hyyrö
  • Ayumi Shinohara
  • Masayuki Takeda
  • Kenta Nakai
  • Satoru Miyano
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3245)

Abstract

We consider the problem of discovering the optimal pair of substring patterns with bounded distance α, from a given set S of strings. We study two kinds of pattern classes, one is in form \(p \land_\alpha q\) that are interpreted as cooperative patterns within α distance, and the other is in form \(p \land_\alpha \lnot q\) representing competing patterns, with respect to S. We show an efficient algorithm to find the optimal pair of patterns in O(N2) time using O(N) space. We also present an O(m2N2) time and O(m2N) space solution to a more difficult version of the optimal pattern pair discovery problem, where m denotes the number of strings in S.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Shunsuke Inenaga
    • 1
  • Hideo Bannai
    • 2
  • Heikki Hyyrö
    • 3
  • Ayumi Shinohara
    • 3
    • 5
  • Masayuki Takeda
    • 4
    • 5
  • Kenta Nakai
    • 2
  • Satoru Miyano
    • 2
  1. 1.Department of Computer ScienceUniversity of HelsinkiFinland
  2. 2.Human Genome Center, Institute of Medical ScienceThe University of TokyoTokyoJapan
  3. 3.PRESTOJapan Science and Technology Agency (JST) 
  4. 4.SORSTJapan Science and Technology Agency (JST) 
  5. 5.Department of InformaticsKyushu University 33FukuokaJapan

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