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)


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.


Parallel Algorithm Quadratic Space Parallel Time Communication Round Coarse Granularity 
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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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