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© Oxford University Press

Parallel hardware for sequence comparison and alignment

Richard Hughey

Computer Engineering, University of California Santa Cruz, CA 95064, USAE-mail: rph{at}cse.ucsc.edu

Sequence comparison, a vital research tool in computational biology, is based on a simple O(n2) algorithm that easily maps to a linear array of processors. This paper reviews and compares high-performance sequence analysis on general-purpose supercomputers and single-purpose reconfigurable, and programmable co-processors. The difficulty of comparing hardware from published performance figures is also noted.

Received on January 25, 1996; accepted on September 6, 1996

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