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)

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).

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References

  1. 1.
    Baeza-Yates, R.A., Gonnet, G.H.: All-against-all sequence matching. Rep. Dept. of CS, U. de Chile (1990)Google Scholar
  2. 2.
    Baeza-Yates, R.A., Gonnet, G.H.: A fast algorithm on average for all-against-all sequence matching. In: Proc. SPIRE/CRIWG 1999, pp. 16–23 (1999)Google Scholar
  3. 3.
    Barsky, M., Stege, U., Thomo, A., Upton, C.A.: A New Algorithm for Fast All-Against-All Substring Matching (2006), http://www.cs.uvic.ca/~mgbarksy/apbt.pdf
  4. 4.
    Gusfield, D.: Algorithms on Strings, Trees and Sequences. Cambridge University Press, Cambridge (1997)MATHCrossRefGoogle Scholar
  5. 5.
    Pevzner, P., Sze, S.H.: Combinatorial approaches to finding subtle signals in DNA sequences. In: Proc. ISMB 2000, pp. 269–278 (2000)Google Scholar
  6. 6.
    Ukkonen, E.: Algorithms for approximate string matching. Information and Control 64, 100–118 (1985)MATHCrossRefMathSciNetGoogle Scholar
  7. 7.
    Ukkonen, E.: Approximate string matching over suffix trees. In: Apostolico, A., Crochemore, M., Galil, Z., Manber, U. (eds.) CPM 1993. LNCS, vol. 684, pp. 228–242. Springer, Heidelberg (1993)CrossRefGoogle Scholar
  8. 8.
    Vilo, J.: Pattern Discovery from Biosequences. PhD Thesis, Series of Publications A, Report A-2002-3 U. of Helsinki, Finland (2002)Google Scholar
  9. 9.
    Virus Orthologous Clusters database at Viral Bioinformatics Resource Center, U. of Victoria, Canada, http://athena.bioc.uvic.ca

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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