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Accelerating BLASTP on the cell broadband engine

: Zhang, Huiliang; Schmidt, Bertil; Müller-Wittig, Wolfgang K.


Chetty, M. ; International Association for Pattern Recognition -IAPR-:
Pattern recognition in bioinformatics. Third IAPR International Conference, PRIB 2008 : Melbourne, Australia, October 15-17, 2008; Proceedings
Berlin: Springer, 2008 (Lecture notes in bioinformatics 5265)
ISBN: 3-540-88434-3
ISBN: 978-3-540-88434-7
ISSN: 0302-9743
International Conference on Pattern Recognition in Bioinformatics (PRIB) <3, 2008, Melbourne>
Fraunhofer IGD ()
Bioinformatics; hardware; runtime performance

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.