Title :
Parallel sequence comparison and alignment
Author_Institution :
California Univ., Santa Cruz, CA, USA
Abstract :
Sequence comparisons, 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
Keywords :
biology computing; computational complexity; coprocessors; genetics; parallel algorithms; parallel architectures; reconfigurable architectures; alignment; computational biology; general-purpose supercomputers; parallel sequence comparison; simple O(n2) algorithm; single-purpose reconfigurable programmable co-processors; Coprocessors; Costs; Databases; Dynamic programming; Field programmable gate arrays; Genomics; Hardware; Registers; Sequences; Supercomputers;
Conference_Titel :
Application Specific Array Processors, 1995. Proceedings. International Conference on
Conference_Location :
Strasbourg
Print_ISBN :
0-8186-7109-2
DOI :
10.1109/ASAP.1995.522916
