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

  • Marina Barsky
  • Ulrike Stege
  • Alex Thomo
  • Chris Upton
Conference paper

DOI: 10.1007/11880561_31

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4209)
Cite this paper as:
Barsky M., Stege U., Thomo A., Upton C. (2006) A New Algorithm for Fast All-Against-All Substring Matching. In: Crestani F., Ferragina P., Sanderson M. (eds) String Processing and Information Retrieval. SPIRE 2006. Lecture Notes in Computer Science, vol 4209. Springer, Berlin, Heidelberg

Abstract

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(NMK2).

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

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

Personalised recommendations