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Fast Sequence Similarity Computing with LCS on LARPBS

  • Xiaohua Xu
  • Ling Chen
  • Ping He
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3759)

Abstract

The problem of the longest common subsequence (LCS) is a fundamental problem in sequence alignment. In this paper, we first present fast parallel algorithms for sequence similarity with LCS. For two sequences of lengths m and n (m n), the algorithm uses n processors and costs O(m) computation time. Time-area cost of the algorithm is O(mn) which reaches optimality. Based on this algorithm, we also give a fast parallel algorithm which can compute the length of LCS in O(logm) time. To our best knowledge, this is the fastest one among the parallel LCS algorithms on array architectures.

Keywords

Parallel Algorithm Systolic Array Longe Common Subsequence Longe Common Subsequence Primitive Operation 
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.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Xiaohua Xu
    • 1
  • Ling Chen
    • 2
    • 3
  • Ping He
    • 2
  1. 1.Department of Computer Science and EngineeringNanjing University of Aeronautics and AstronauticsNanjingChina
  2. 2.Department of Computer ScienceYangzhou UniversityYangzhouChina
  3. 3.National Key Lab of Novel Software TechNanjing UniversityNanjingChina

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