Accelerating BLASTP on the Cell Broadband Engine

  • Huiliang Zhang
  • Bertil Schmidt
  • Wolfgang Müller-Wittig
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5265)

Abstract

The enormous growth of biological sequence databases has caused bioinformatics to be rapidly moving towards a data-intensive, computational science. As a result, the computational power needed by bioinformatics applications is growing rapidly as well. The recent emergence of low cost parallel accelerator technologies has made it possible to reduce execution times of many bioinformatics applications. In this paper, we demonstrate how the PlayStation®3, powered by the Cell Broadband Engine, can be used as an efficient computational platform to accelerate the popular BLASTP algorithm.

Keywords

Query Sequence Direct Memory Access Query Length Bioinformatics Application Subject Sequence 
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

  • Huiliang Zhang
    • 1
  • Bertil Schmidt
    • 1
  • Wolfgang Müller-Wittig
    • 1
  1. 1.School of Computer EngineeringNanyang Technological UniversitySingapore

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