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© IRL Press

Parallel computation and FASTA: confronting the problem of parallel database search for a fast sequence comparison algorithm

Perry L. Miller , Prakash M. Nadkarni and Nicholas M. Carriero 1

Department of Anesthesiology, Yale University School of Medicine 333 Cedar Street, New Haven, CT 06510
1Department of Computer Science, Yale University 51 Prospect Street, New Haven, CT 06511, USA

We have parallelized the FASTA algorithm for biological sequence comparison using Linda, a machine-independent parallel programming language. The resulting parallel program runs on a variety of different parallel machines. A straightforward parallelization strategy works well if the amount of computation to be done is relatively large. When the amount of computation is reduced, however, disk I/O becomes a bottleneck which may prevent additional speed-up as the number of processors is increased. The paper describes the parallelization of FASTA, and uses FASTA to illustrate the I/O bottleneck problem that may arise when performing parallel database search with a fast sequence comparison algorithm. The paper also describes several program design strategies that can help with this problem. The paper discusses how this bottleneck is an example of a general problem that may occur when parallelizing, or otherwise speeding up, a time-consuming computation.

Received on July 25, 1990; accepted on October 15, 1990

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 International Journal of High Performance Computing ApplicationsHome page
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International Journal of High Performance Computing Applications, June 1, 1992; 6(2): 147 - 163.
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