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

P L Miller·P M Nadkarni·N M Carriero
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Abstract

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 straight-forward 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.

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AlgorithmsAmino Acid SequenceComputer SystemsMathematical ComputingMolecular Sequence DataProgramming LanguagesSoftware DesignJournal ArticleResearch Support, U.S. Gov't, P.H.S.

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P L Miller, P M Nadkarni, N M Carriero. 1991. Parallel computation and FASTA: confronting the problem of parallel database search for a fast sequence comparison algorithm.. https://doi.org/10.1093/bioinformatics%2F7.1.71

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