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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

ISBN: 978-989-8425-90-4

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 - Volume 1: BIOINFORMATICS, (BIOSTEC 2012) ISBN 978-989-8425-90-4, 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 - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)},
year={2012},
pages={182-187},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003769801820187},
isbn={978-989-8425-90-4},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)
TI - PERFORMANCE STUDY OF PARALLEL HYBRID MULTIPLE PATTERN MATCHING ALGORITHMS FOR BIOLOGICAL SEQUENCES
SN - 978-989-8425-90-4
AU - S. Kouzinopoulos, C.
AU - D. Michailidis, P.
AU - G. Margaritis, K.
PY - 2012
SP - 182
EP - 187
DO - 10.5220/0003769801820187

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