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Parallel DNA Sequence Alignment on the Cell Broadband Engine

  • Adrianto Wirawan
  • Kwoh Chee Keong
  • Bertil Schmidt
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4967)

Abstract

Sequence alignment is one of the most important techniques in Bioinformatics. Although efficient dynamic programming algorithms exist for this problem, the alignment of very long DNA sequences still requires significant time on traditional computer architectures. In this paper, we present a scalable and efficient mapping of DNA sequence alignment onto the Cell BE multi-core architecture. Our mapping uses two types of parallelization techniques: (i) SIMD vectorization within a processor and (ii) wavefront parallelization between processors.

Keywords

Parallel Algorithm Single Instruction Multiple Data Direct Memory Access Dynamic Programming Matrix Cell Broadband Engine 
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 2008

Authors and Affiliations

  • Adrianto Wirawan
    • 1
  • Kwoh Chee Keong
    • 1
  • Bertil Schmidt
    • 2
  1. 1.School of Computer EngineeringNanyang Technological UniversitySingapore
  2. 2.University of New South WalesSingapore

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