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.
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Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic Local Alignment Search Tool. J. Mol. Biol. 215(3), 403–410 (1990)
Altschul, S.F., et al.: Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs. Nucleic Acid Research 25(7), 3389–3402 (1997)
Cameron, M., Williams, H.E., Cannane, A.: A Deterministic Finite Automaton for Faster Protein Hit Detection in BLAST. Journal of Computational Biology 13(4), 965–978 (2006)
Cameron, M., Williams, H.E., Cannane, A.: Improved Gapped Alignment in BLAST. IEEE Trans. Computational Biology and Bioinformatics 1(3), 116–129 (2004)
Jacob, A., Lancaster, J., Harris, B., Buhler, J., Chamberlain, R.: Mercury BLASTP: Accelerating Protein Sequence Alignment. ACM Transactions on Reconfigurable Technology and Systems(to appear, 2008)
Kahle, J.A., et al.: Introduction the Cell multiprocessor. IBM Journal of Research and Development 49(4/5), 598–604 (2005)
Kent, W.J.: BLAT – The BLAST-like Alignment Tool. Genome Research 12(4), 656–664 (2002)
Kistler, M., Perrone, F., Petrini, F.: Cell multiprocessor communication network: built for speed. IEEE Micro. 26(3), 10–23 (2006)
Li, M., Ma, B., Kisman, D., Tromp, J.: Patternhunter II: Highly Sensitive and Fast Homology Search. J. Bioinformatics and Computational Biology 2(3), 417–439 (2004)
Oehmen, C., Nieplocha, J.: ScalaBLAST: A scalable implementation of BLAST for high-performance data-intensive bioinformatics analysis. IEEE Transactions on Parallel and Distributed Systems 17(8), 740–749 (2006)
Pham, D., et al.: The design and implementation of a first-generation Cell processor. In: Proceedings IEEE ISSCC 2005, San Francisco, CA, pp. 184–185 (2005)
Sachdeva, V., Kistler, M., Speight, E., Tzeng, T.H.K.: Exploring the viability of the Cell Broadband Engine for bioinformatics applications. In: 6th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2007), Long Beach, CA (2007)
Smith, T.F., Waterman, M.S.: Identification of Common Molecular Subsequences. J. Mol. Biol. 147, 195–197 (1981)
Wirawan, A., Kwoh, C.K., Schmidt, B.: Parallel DNA Sequence Alignment on the Cell Broadband Engine. In: Wyrzykowski, R., Dongarra, J., Karczewski, K., Waśniewski, J. (eds.) PPAM 2007. LNCS, vol. 4967. Springer, Heidelberg (to appear, 2008)
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Zhang, H., Schmidt, B., Müller-Wittig, W. (2008). Accelerating BLASTP on the Cell Broadband Engine. In: Chetty, M., Ngom, A., Ahmad, S. (eds) Pattern Recognition in Bioinformatics. PRIB 2008. Lecture Notes in Computer Science(), vol 5265. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88436-1_39
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DOI: https://doi.org/10.1007/978-3-540-88436-1_39
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