EXPERIMENTAL RESULTS ON MULTIPLE PATTERN MATCHING ALGORITHMS FOR BIOLOGICAL SEQUENCES

Charalampos S. Kouzinopoulos; Panagiotis D. Michailidis; Konstantinos G. Margaritis

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Paper

EXPERIMENTAL RESULTS ON MULTIPLE PATTERN MATCHING ALGORITHMS FOR BIOLOGICAL SEQUENCES

Topics: Algorithms and Software Tools

In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - BIOINFORMATICS, 274-277, 2011 , Rome, Italy

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

Affiliation: University of Macedonia, Greece

Keyword(s): Algorithms, Multiple pattern matching, Multiple keyword matching, String searching, Biological sequence databases.

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

Abstract: With the remarkable increase in the number of DNA and proteins sequences, it is very important to study the performance of multiple pattern matching algorithms when querying sequence patterns in biological sequence databases. In this paper, we present a performance study of the running time of well known multiple pattern matching algorithms on widely used biological sequence databases containing the building blocks of nucleotides (in the case of nucleic acid sequence databases) and amino acids (in the case of protein sequence databases).

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Paper citation in several formats:

S. Kouzinopoulos, C.; D. Michailidis, P. and G. Margaritis, K. (2011). EXPERIMENTAL RESULTS ON MULTIPLE PATTERN MATCHING ALGORITHMS FOR BIOLOGICAL SEQUENCES. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - BIOINFORMATICS, (BIOSTEC 2011) ISBN 978-989-8425-36-2; ISSN 2184-4305, SciTePress, pages 274-277. DOI: 10.5220/0003133202740277

@conference{bioinformatics11,
author={Charalampos {S. Kouzinopoulos}. and Panagiotis {D. Michailidis}. and Konstantinos {G. Margaritis}.},
title={EXPERIMENTAL RESULTS ON MULTIPLE PATTERN MATCHING ALGORITHMS FOR BIOLOGICAL SEQUENCES},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - BIOINFORMATICS, (BIOSTEC 2011)},
year={2011},
pages={274-277},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003133202740277},
isbn={978-989-8425-36-2},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - BIOINFORMATICS, (BIOSTEC 2011)
TI - EXPERIMENTAL RESULTS ON MULTIPLE PATTERN MATCHING ALGORITHMS FOR BIOLOGICAL SEQUENCES
SN - 978-989-8425-36-2
IS - 2184-4305
AU - S. Kouzinopoulos, C.
AU - D. Michailidis, P.
AU - G. Margaritis, K.
PY - 2011
SP - 274
EP - 277
DO - 10.5220/0003133202740277
PB - SciTePress