A New Algorithm for Fast All-Against-All Substring Matching

  • Marina Barsky
  • Ulrike Stege
  • Alex Thomo
  • Chris Upton
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4209)


We present a new and efficient algorithm to solve the ’threshold all vs. all’ problem, which involves searching of two strings (with length N and M respectively) for finding all maximal approximate matches of length at least S and with up to K differences. The algorithm is based on a novel graph model, and it solves the problem in time O(NMK 2).


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Marina Barsky
    • 1
  • Ulrike Stege
    • 1
  • Alex Thomo
    • 1
  • Chris Upton
    • 1
  1. 1.University of VictoriaCanada

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