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International Journal of High Performance Computing Applications
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Regular Paper: A Study of Architectural Optimization Methods in Bioinformatics Applications

G. Tan

KEY LABORATORY OF COMPUTER SYSTEM AND ARCHITECTURE, INSTITUTE OF COMPUTING TECHNOLOGY, CHINESE ACADEMY OF SCIENCES, BEIJING, CHINA,TGM{at}NCIC.AC.CN

L. Xu

KEY LABORATORY OF COMPUTER SYSTEM AND ARCHITECTURE, INSTITUTE OF COMPUTING TECHNOLOGY, CHINESE ACADEMY OF SCIENCES, BEIJING, CHINA

Z. Dai

KEY LABORATORY OF COMPUTER SYSTEM AND ARCHITECTURE, INSTITUTE OF COMPUTING TECHNOLOGY, CHINESE ACADEMY OF SCIENCES, BEIJING, CHINA

S. Feng

KEY LABORATORY OF COMPUTER SYSTEM AND ARCHITECTURE, INSTITUTE OF COMPUTING TECHNOLOGY, CHINESE ACADEMY OF SCIENCES, BEIJING, CHINA

N. Sun

KEY LABORATORY OF COMPUTER SYSTEM AND ARCHITECTURE, INSTITUTE OF COMPUTING TECHNOLOGY, CHINESE ACADEMY OF SCIENCES, BEIJING, CHINA

Studies in the optimization of sequence alignment have been carried out in bioinformatics. In this paper, we have focused on two aspects: memory usage and execution time. Our study suggests that cache memory does not have a significant effect on system performance. Our attention then turns to optimize Smith—Waterman's algorithm. Two instruction level methods have been proposed and 2—8 fold speed improvements have been observed after the optimization has been implemented. Further improvements on system performance have been achieved by overlapping computation with system I/O usage.

Key Words: bioinformatics • sequence alignment • cache memory • instruction level parallelism • I/O overlapping

International Journal of High Performance Computing Applications, Vol. 21, No. 3, 371-384 (2007)
DOI: 10.1177/1094342007078175
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