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Comparative Analysis of Similarity Check Mechanism for Motif Extraction

Makolo, A. and Osofisan, A. O. and Adebiyi, Ezekiel Comparative Analysis of Similarity Check Mechanism for Motif Extraction. African Journal of Computing & ICT, 5 (1). pp. 53-58. ISSN 2006-1781

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Abstract

In this work, a comparative analysis of the similarity check mechanism used in the most effective algorithm for mining simple motifs GEMS (Gene Enrichment Motif Searching) and that used in a popular multi-objective genetic algorithm, MOGAMOD (Multi-Objective Genetic Algorithm for Motif Discovery) was done. In our previous work, we had reported the implementation of GEMS on suffix tree –Suffix Tree Gene Enrichment Motif Searching (STGEMS) and shown the linear asymptotic runtime achieved. Here, we attempt to empirically proof the high sensitivity of the resulting algorithm, STGEMS in mining motifs from challenging sequences like we have in Plasmodium falciparum. The results obtained validates the high sensitivity of the similarity check mechanism employed in GEMS and also shows that a careful deployment of this mechanism in the multi-objective genetic algorithm, improved the sensitiv

Item Type: Article
Uncontrolled Keywords: Motifs, GEMS, MOGAMOD, STGEMS, Suffix tree.
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Divisions: Faculty of Engineering, Science and Mathematics > School of Electronics and Computer Science
Depositing User: Mrs Patricia Nwokealisi
Date Deposited: 18 May 2017 11:16
Last Modified: 18 May 2017 11:16
URI: http://eprints.covenantuniversity.edu.ng/id/eprint/8143

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