Bio-sequence analysis with cradle's 3SoC™ software scalable system on chip

Authors:
Xiandong Meng;Vipin Chaudhary
Affiliations:
Wayne State University, MI, Detroit;Wayne State University Detroit, MI
Venue:
Proceedings of the 2004 ACM symposium on Applied computing
Year:
2004

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Abstract

With the dramatically increasing amounts of genomic sequence database, there is a need for faster and more sensitive searching for sequence similarity analysis. The Smith-Waterman algorithm, which utilizes dynamic programming, is a common method for performing exact local alignments between two protein or DNA sequences. The Smith-Waterman algorithm is exhaustive and generally considered to be the most sensitive, but long computation times limit the use of this algorithm. This paper presents a preliminary implementation of Smith-Waterman algorithm using a new chip multiprocessor architecture with multiple Digital Signal Processors (DSP) on a single chip leading to high performance at low cost.