FUZZY CONCEPT LATTICE-BASED APPROACH FOR REACTIVE MOTIFS DISCOVERY

Thanapat Kangkachit, Kitsana Waiyamai

2012

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 method 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.

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Paper Citation


in Harvard Style

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


in Bibtex Style

@conference{bioinformatics12,
author={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},
}


in EndNote Style

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 - Waiyamai K.
PY - 2012
SP - 326
EP - 330
DO - 10.5220/0003787503260330