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.
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© 2008 Springer-Verlag Berlin Heidelberg
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Wirawan, A., Keong, K.C., Schmidt, B. (2008). Parallel DNA Sequence Alignment on the Cell Broadband Engine. In: Wyrzykowski, R., Dongarra, J., Karczewski, K., Wasniewski, J. (eds) Parallel Processing and Applied Mathematics. PPAM 2007. Lecture Notes in Computer Science, vol 4967. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-68111-3_132
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DOI: https://doi.org/10.1007/978-3-540-68111-3_132
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-68105-2
Online ISBN: 978-3-540-68111-3
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