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Authors: Thanapat Kangkachit and Kitsana Waiyamai

Affiliation: Kasetsart University, Thailand

ISBN: 978-989-8425-90-4

Keyword(s): Complete substitution group, Fuzzy concept lattice, Reactive motifs, Enzyme function classification, Binding and catalytic site, Amino acid sustitution matrix, Biochemical knowledge.

Related Ontology Subjects/Areas/Topics: Bioinformatics ; Biomedical Engineering ; Data Mining and Machine Learning ; Sequence Analysis ; Structure Prediction

Abstract: Reactive motifs are short conserved regions discovered from binding and catalytic sites of enzymes sequences. Thus, reactive motifs provide more biological meaning than statistic-based motifs because they are directly extracted from where the chemical reaction mechanism occurs. Main problem of discovering reactive motifs is that only 4.94% enzymes sequences contain sites information. To overcome this problem, we present fuzzy concept lattice-based (FCL-based) method for discovering more general reactive motifs by incorporating biochemical knowledge. Fuzzy concept lattices are used to represent both binary and multi-value biochemical knowledge. The fuzzy concept lattice Join operator is applied to determine complete substitution groups that obtains more general reactive motifs. Experiments are conducted among different methods of determining complete substitution groups: FCL-based, concecpt lattice-based (CL-based) and similarity-based method. Experimental results show that FCL-based m ethod significantly outperforms other methods in term of coverage value and F-measure with SVM learning algorithm. Therefore, fuzzy concept lattice provides more efficient computational support for complete substitution groups operation than that of other existing methods. (More)

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Paper citation in several formats:
Kangkachit, T.; Kangkachit, T. and Waiyamai, K. (2012). FUZZY CONCEPT LATTICE-BASED APPROACH FOR REACTIVE MOTIFS DISCOVERY.In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012) ISBN 978-989-8425-90-4, pages 326-330. DOI: 10.5220/0003787503260330

@conference{bioinformatics12,
author={Thanapat Kangkachit. and Thanapat Kangkachit. and Kitsana Waiyamai.},
title={FUZZY CONCEPT LATTICE-BASED APPROACH FOR REACTIVE MOTIFS DISCOVERY},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2012)},
year={2012},
pages={326-330},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003787503260330},
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 - FUZZY CONCEPT LATTICE-BASED APPROACH FOR REACTIVE MOTIFS DISCOVERY
SN - 978-989-8425-90-4
AU - Kangkachit, T.
AU - Kangkachit, T.
AU - Waiyamai, K.
PY - 2012
SP - 326
EP - 330
DO - 10.5220/0003787503260330

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