Parallel DNA sequence alignment on the cell broadband engine

Authors:
Adrianto Wirawan;Kwoh Chee Keong;Bertil Schmidt
Affiliations:
School of Computer Engineering, Nanyang Technological University, Singapore;School of Computer Engineering, Nanyang Technological University, Singapore;University of New South Wales, Singapore
Venue:
PPAM'07 Proceedings of the 7th international conference on Parallel processing and applied mathematics
Year:
2007

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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 multicore architecture. Our mapping uses two types of parallelization techniques: (i) SIMD vectorization within a processor and (ii) wavefront parallelization between processors.