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Using a DSM application to locally align DNA sequences | IEEE Conference Publication | IEEE Xplore

Using a DSM application to locally align DNA sequences


Abstract:

Sequence comparison is a basic operation in DNA sequencing projects, and most sequence comparison methods used are based on heuristics, that are faster but do not produce...Show More

Abstract:

Sequence comparison is a basic operation in DNA sequencing projects, and most sequence comparison methods used are based on heuristics, that are faster but do not produce optimal alignments. Recently, many organisms have had their DNA entirely sequenced, and this reality presents the need for comparing long DNA sequences, which is a challenging task due to its high demands for computational power and memory. Although DSM is presented as a feasible parallel programming paradigm, much of the work in DSM is validated by benchmarks and there are only a few examples of real parallel applications running on DSM systems. In this article, we present and evaluate a parallelization strategy for implementing a local DNA sequence alignment algorithm. This strategy was implemented in JIAJIA, a scope consistent software DSM system. Our results on an eight-machine cluster presented very good speedups, which are comparable with the ones obtained with MPI, showing that our parallelization strategy and programming support were appropriate.
Date of Conference: 19-22 April 2004
Date Added to IEEE Xplore: 27 September 2004
Print ISBN:0-7803-8430-X
Conference Location: Chicago, IL, USA

References

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