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A systolic array processor for biological information signal processing

Chow, E. T. and Hunkapiller, Tim and Peterson, J. C. and Zimmerman, B. A. and Waterman, M. S. (1991) A systolic array processor for biological information signal processing. In: ICS '91 Proceedings of the 5th international conference on Supercomputing. ACM , New York, NY, pp. 216-223. ISBN 0-89791-434-1 . https://resolver.caltech.edu/CaltechAUTHORS:20160913-155820912

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Abstract

The Biological Information Signal Processing (BISP) is a system for high speed sequence comparisons designed to support the computation requirements for mapping and sequencing the human and other genomes. The heart of a BISP system is a versatile processor chip that can conduct the most time consuming sequence comparison functions, establishing both global and local relationships between two DNA or protein sequences. Because of the application’s strong computation and communication requirements, a programmable systolic array architecture was developed. A BISP system can include a large number of processing elements; the initial BISP demonstration system consists of 768 BISP elements, capable of delivering more than 6.25 x 10^9 integer operations per second. The system can be expanded to include over 4,000 elements, This paper describes the comparison algorithm and outlines the BISP chip and system designs. Estimated performance of the BISP system is compared with several different computer architectures.


Item Type:Book Section
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http://dx.doi.org/10.1145/109025.109081DOIChapter
http://dl.acm.org/citation.cfm?doid=109025.109081PublisherChapter
Additional Information:© 1991 ACM. The research described in this paper was carried out by the Jet Propulsion Laboratory, California Institute of Technology, and University of Southern California, and was sponsored by National Science Foundation, Department of Energy, and National Institutes of Health.
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Record Number:CaltechAUTHORS:20160913-155820912
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20160913-155820912
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ID Code:70320
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Deposited By: Kristin Buxton
Deposited On:29 Sep 2016 23:54
Last Modified:03 Oct 2019 10:29

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