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Fast Scalable Algorithm on LARPBS for Sequence Alignment

  • Ling Chen
  • Chen Juan
  • Yi Pan
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3759)

Abstract

Linear array with reconfigurable pipelined bus system (LARPBS) is a parallel computational model based on the optical bus system. In this paper, an O(1) time algorithm on LARPBS for prefix computation based on the maximum operation is presented. We also present a fast and efficient sequence alignment algorithm on LARPBS. For two sequences with length of m, n respectively, the algorithm can be implemented in O(mn/p) time with p processors(1≤p≤max{m,n}). Since the time complexity of the algorithm can be adjusted by choosing different number of processors p , the algorithm is highly scalable.

Keywords

Time Complexity Parallel Algorithm Systolic Array Optimal Alignment Longe Common Subsequence 
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

  • Ling Chen
    • 1
    • 2
  • Chen Juan
    • 1
  • Yi Pan
    • 3
  1. 1.Department of Computer ScienceYangzhou UniversityYangzhouP.R. China
  2. 2.National Key Lab of Novel Software TechNanjing UniversityNanjingP.R. China
  3. 3.Department of Computer ScienceGeorgia State UniversityAtlantaU.S.A.

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