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High-speed implementation of Smith-Waterman algorithm for DNA sequence scanning in VLSI

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2 Author(s)
Chao Cheng ; Dept. of Electr. & Comput. Engr., Univ. of Minnesota, Minneapolis, MN ; Parhi, K.K.

In this paper, a novel pipelined algorithm is applied in the hardware implementation of Smith-Waterman algorithm. The proposed algorithm can cut down the computation time from O(m+n) to O(m+n/J), where J is the pipeline level, m and n are the lengths of the query sequence and subject sequence respectively. It's obvious that if the length of subject sequence is much larger than the query sequence, i.e., n>>m, the computation of scanning protein sequences will be speeded up by a factor of J.

Published in:

Signals, Systems and Computers, 2008 42nd Asilomar Conference on

Date of Conference:

26-29 Oct. 2008