Parallel hardware for sequence comparison and alignment.
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.
Hughey
R
R
University of California, Santa Cruz 95064, USA. rph@cse.ucsc.edu
D000465:Algorithms; D003199:Computer Systems; D003201:Computers; D016208:Databases, Factual; D016045:Human Genome Project; D006801:Humans; D016415:Sequence Alignment / Q000379:methods* / Q000706:statistics & numerical data