Optimization of MISCORE-based Motif Identification Systems

Lee, Nung Kion and Wang, Dianhui (2009) Optimization of MISCORE-based Motif Identification Systems. In: Bioinformatics and Biomedical Engineering, 2009. ICBBE 2009. 3rd International Conference on, 11-13 June 2009, Beijing.

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Abstract

Identification of motifs in DNA sequences using classification techniques is one of computational approaches to discovering novel binding sites. In the previous work [16], we proposed a simple and effective method for motif detection using a single crisp rule governed by a mismatch-based matrix similarity score (MISCORE). In this paper, we consider the problem of finding suitable motif cut-off value for MISCORE-based motif identification systems using cost-sensitivity metric. We utilize phylogenetic footprinting data to estimate the parameters in the cost function. We also extend the MISCORE to include entropy to weigh each motif model position to minimize the false positive rate. The performance evaluation is done by using artificial and real DNA sequences. The results demonstrate the feasibility and usefulness of our proposed approach for model based cut-off value estimation.

Item Type: Conference or Workshop Item (Paper)
Uncontrolled Keywords: DNA sequences, motif detection, computational algorithm, MISCORE-based Motif Identification Systems, unimas, university, universiti, Borneo, Malaysia, Sarawak, Kuching, Samarahan, ipta, education, research, Universiti Malaysia Sarawak
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
T Technology > T Technology (General)
Divisions: Academic Faculties, Institutes and Centres > Faculty of Cognitive Sciences and Human Development
Depositing User: Karen Kornalius
Date Deposited: 12 May 2016 04:43
Last Modified: 12 May 2016 04:43
URI: http://ir.unimas.my/id/eprint/11946

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