Parallel Sequence Comparison and Alignment

Authors:
Richard Hughey
Affiliations:
-
Venue:
ASAP '95 Proceedings of the IEEE International Conference on Application Specific Array Processors
Year:
1995

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Abstract

Sequence comparison, a vital research tool in computational biology, is based on a simple O(n**2) 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.