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Pseudo-realtime Pattern Matching: Closing the Gap

  • Raphaël Clifford
  • Benjamin Sach
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6129)

Abstract

We consider the k-difference and k-mismatch problems in the pseudo-realtime model where the text arrives online and the time complexity measure is per arriving character and unamortised. The well-known k-difference/k-mismatch problems are those of finding all alignments of a pattern of length m with a text of length n where the edit/Hamming distance is at most k. Offline, the literature gives efficient solutions in O(nk) and \(O(n \sqrt{k \log k})\) time, respectively. More recently, a pseudo-realtime solution was given for the former in O(k logm) time and the latter in \(O(\sqrt{k \log k}\log m)\) time per arriving text character. Our work improves these complexities to O(k) time for the k-difference problem and \(O(\sqrt{k}\log k + \log m)\) for the k-mismatch problem. In the process of developing the main results, we also give a simple solution with optimal time complexity for performing longest common extension queries in the same pseudo-realtime setting which may be of independent interest.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Raphaël Clifford
    • 1
  • Benjamin Sach
    • 1
  1. 1.Department of Computer ScienceUniversity of BristolUK

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