Advertisement

Finding the Position of the k-Mismatch and Approximate Tandem Repeats

  • Haim Kaplan
  • Ely Porat
  • Nira Shafrir
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4059)

Abstract

Given a pattern P, a text T, and an integer k, we want to find for every position j of T, the index of the k-mismatch of P with the suffix of T starting at position j. We give an algorithm that finds the exact index for each j, and algorithms that approximate it. We use these algorithms to get an efficient solution for an approximate version of the tandem repeats problem with k-mismatches.

Keywords

Tandem Repeat Binary Search String Match Random String Frequent Character 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Abrahamson, K.: Generalized string matching. SIAM J. Comput. 16(6), 1039–1051 (1987)MATHCrossRefMathSciNetGoogle Scholar
  2. 2.
    Amir, A., Lewenstein, M., Porat, E.: Faster algorithms for string matching with k mismatches. J. Algorithms 50(2), 257–275 (2004)MATHCrossRefMathSciNetGoogle Scholar
  3. 3.
    Cole, R., Hariharan, R.: Approximate string matching: A simpler faster algorithm. SIAM J. Comput. 31(6), 1761–1782 (2002)MATHCrossRefMathSciNetGoogle Scholar
  4. 4.
    Crochemore, M., Rytter, W.: Text Algorithms, pp. 27–31. Oxford Univ. Press, New-York (1994)MATHGoogle Scholar
  5. 5.
    Gusfield, D.: Algorithms on strings, trees and sequences: computer science and computational biology. Cambridge University Press, Cambridge (1997)MATHCrossRefGoogle Scholar
  6. 6.
    Karloff, H.J.: Fast algorithms for approximately counting mismatches. Inf. Process. Lett. 48(2), 53–60 (1993)MATHCrossRefMathSciNetGoogle Scholar
  7. 7.
    Landau, G.M., Schmidt, J.P., Sokol, D.: An algorithm for approximate tandem repeats. Journal of Computational Biology 8(1), 1–18 (2001)CrossRefGoogle Scholar
  8. 8.
    Landau, G.M., Vishkin, U.: Efficient string matching in the presence of errors. In: Proc. 26th IEEE Symposium on Foundations of Computer Science, pp. 126–136. IEEE Computer Society, Los Alamitos (1985)Google Scholar
  9. 9.
    Main, M.G., Lorentz, R.J.: An o(n log n) algorithm for finding all repetitions in a string. J. Algorithms 5(3), 422–432 (1984)MATHCrossRefMathSciNetGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Haim Kaplan
    • 1
  • Ely Porat
    • 2
  • Nira Shafrir
    • 1
  1. 1.School of Computer ScienceTel Aviv UniversityTel AvivIsrael
  2. 2.Department of Mathematics and Computer ScienceBar-Ilan UniversityRamat-GanIsrael

Personalised recommendations