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Authors: Charalampos S. Kouzinopoulos 1 ; Panagiotis D. Michailidis 2 and Konstantinos G. Margaritis 1

Affiliations: 1 University of Macedonia, Greece ; 2 University of Western Macedonia, Greece

Keyword(s): Algorithms, Multiple pattern matching, Parallel computing, Hybrid, OpenMP, MPI, Biological sequence databases.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Model Design and Evaluation

Abstract: Multiple pattern matching is widely used in computational biology to locate any number of nucleotides in genome databases. Processing data of this size often requires more computing power than a sequential computer can provide. A viable and cost-effective solution that can offer the power required by computationally intensive applications at low cost is to share computational tasks among the processing nodes of a high performance hybrid distributed and shared memory platform that consists of cluster workstations and multi-core processors. This paper presents experimental results and a theoretical performance model of the hybrid implementations of the Commentz-Walter, Wu-Manber, Set Backward Oracle Matching and the Salmela-Tarhio-Kytöjoki family of multiple pattern matching algorithms when executed in parallel on biological sequence databases.

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Paper citation in several formats:
S. Kouzinopoulos, C., D. Michailidis, P. and G. Margaritis, K. (2012). PERFORMANCE STUDY OF PARALLEL HYBRID MULTIPLE PATTERN MATCHING ALGORITHMS FOR BIOLOGICAL SEQUENCES. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2012) - BIOINFORMATICS; ISBN 978-989-8425-90-4; ISSN 2184-4305, SciTePress, pages 182-187. DOI: 10.5220/0003769801820187

@conference{bioinformatics12,
author={Charalampos {S. Kouzinopoulos} and Panagiotis {D. Michailidis} and Konstantinos {G. Margaritis}},
title={PERFORMANCE STUDY OF PARALLEL HYBRID MULTIPLE PATTERN MATCHING ALGORITHMS FOR BIOLOGICAL SEQUENCES},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2012) - BIOINFORMATICS},
year={2012},
pages={182-187},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003769801820187},
isbn={978-989-8425-90-4},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2012) - BIOINFORMATICS
TI - PERFORMANCE STUDY OF PARALLEL HYBRID MULTIPLE PATTERN MATCHING ALGORITHMS FOR BIOLOGICAL SEQUENCES
SN - 978-989-8425-90-4
IS - 2184-4305
AU - S. Kouzinopoulos, C.
AU - D. Michailidis, P.
AU - G. Margaritis, K.
PY - 2012
SP - 182
EP - 187
DO - 10.5220/0003769801820187
PB - SciTePress

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