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Local DNA sequence alignment in a cluster of workstations: Algorithms and tools

Journal of the Brazilian Computer Society volume 10, pages 81–88 (2004)Cite this article

Abstract

Distributed Shared Memory systems allow the use of the shared memory programming paradigm in distributed architectures where no physically shared memory exist. Scope consistent software DSMs provide a relaxed memory model that reduces the coherence overhead by ensuring consistency only at synchronization operations, on a per-lock basis. Much of the work in DSM systems is validated by benchmarks and there are only a few examples of real parallel applications running on DSM systems. Sequence comparison is a basic operation in DNA sequencing projects, and most of sequence comparison methods used are based on heuristics, that are faster but do not produce optimal alignments. Recently, many organisms 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. In this article, we present and evaluate a parallelization strategy for implementing a sequence alignment algorithm for long sequences. This strategy was implemented in JIAJIA, a scope consistent software DSM system. Our results on an eight-machine cluster presented good speedups, showing that our parallelization strategy and programming support were appropriate.

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Authors and Affiliations

  1. Department of Computer Science, University of Brasilia, Brazil

    Alba Cristina M. A. Melo, Maria Emilia M. T. Walter, Renata Cristina F. Melo, Marcelo N. P. Santana & Rodolfo B. Batista

  2. Campus Universitario-ICC-Norte Subsolo, Asa Norte, Brasilia, Brazil

    Alba Cristina M. A. Melo, Maria Emilia M. T. Walter, Renata Cristina F. Melo, Marcelo N. P. Santana & Rodolfo B. Batista

Authors
  1. Alba Cristina M. A. Melo
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  2. Maria Emilia M. T. Walter
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  3. Renata Cristina F. Melo
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  4. Marcelo N. P. Santana
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  5. Rodolfo B. Batista
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Open Access This article is distributed under the terms of the Creative Commons Attribution 2.0 International License ( https://creativecommons.org/licenses/by/2.0 ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Melo, A.C.M.A., Walter, M.E.M.T., Melo, R.C.F. et al. Local DNA sequence alignment in a cluster of workstations: Algorithms and tools. J Braz Comp Soc 10, 81–88 (2004). https://doi.org/10.1007/BF03192360

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