Microparallelism and high-performance protein matching
Supercomputing '95 Proceedings of the 1995 ACM/IEEE conference on Supercomputing
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Memory system characterization of commercial workloads
Proceedings of the 25th annual international symposium on Computer architecture
Execution characteristics of desktop applications on Windows NT
Proceedings of the 25th annual international symposium on Computer architecture
Computer architecture (2nd ed.): a quantitative approach
Computer architecture (2nd ed.): a quantitative approach
Automatic Performance Tuning in the UHFFT Library
ICCS '01 Proceedings of the International Conference on Computational Sciences-Part I
An Analysis of Cache Performance of Multimedia Applications
IEEE Transactions on Computers
Sparsity: Optimization Framework for Sparse Matrix Kernels
International Journal of High Performance Computing Applications
Exploiting performance characterization of BLAST in the grid
Cluster Computing
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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.