Swasad: An Asic Design For High Speed Dna Sequence Matching

Authors:
Tony Han;Sri Parameswaran
Affiliations:
Computer Science and Electrical Engineering, The University of Queensland, QLD 4072 , Australia;Computer Science and Engineering, The University of New South Wales, NSW 2052, Australia
Venue:
ASP-DAC '02 Proceedings of the 2002 Asia and South Pacific Design Automation Conference
Year:
2002

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Abstract

This paper presents the Smith and Waterman Algorithm-Specific ASIC Design (SWASAD) project. This is a hardware solution that implements the S&W algorithm. The SWASAD is an improved implementation of the Biological Information Signal Processor (BISP) design [1], The SWASAD chip fabricated on a 0.5 µ process achieves 3200 million Matrix Cells Per Second (MCPS) per chip, with a layout size of 7.1 mm by 7.1 mm. This is a large improvement over existing designs and improves data throughput by using a smaller datawidth.