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A Parallel Wavefront Algorithm for Efficient Biological Sequence Comparison

  • C. E. R. Alves
  • E. N. Cáceres
  • F. Dehne
  • S. W. Song
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2668)

Abstract

In this paper we present a parallel wavefront algorithm for computing an alignment between two strings A and C, with |A| = m and |C| = n. On a distributed memory parallel computer of p processors each with O((m + n)/p) memory, the proposed algorithm requires O(p) communication rounds and O(mn/p) local computing time. The novelty of this algorithm is based on a compromise between the workload of each processor and the number of communication rounds required, expressed by a parameter called α. The proposed algorithm is expressed in terms of this parameter that can be tuned to obtain the best overall parallel time in a given implementation. We show very promising experimental results obtained on a 64-node Beowulf machine. A characteristic of the wavefront communication requirement is that each processor communicates with few other processors. This makes it very suitable as a potential application for grid computing.

Keywords

Parallel Algorithm Quadratic Space Parallel Time Communication Round Coarse Granularity 
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 2003

Authors and Affiliations

  • C. E. R. Alves
    • 1
  • E. N. Cáceres
    • 2
  • F. Dehne
    • 3
  • S. W. Song
    • 4
  1. 1.Universidade São Judas TadeuSão PauloBrazil
  2. 2.Universidade Federal de Mato Grosso do SulCampo GrandeBrazil
  3. 3.Carleton University - School of Computer ScienceOttawaCanada
  4. 4.Universidade de São PauloSão PauloBrazil

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