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Species motif extraction using LPBS


Syed-Abdullah, Sharifah Lailee and Harun, Hazaruddin (2013) Species motif extraction using LPBS. In: 4th International Conference on Computing and Informatics (ICOCI 2013), 28 -30 August 2013, Kuching, Sarawak, Malaysia.

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Abstract

This paper presents the use of the ̳Linear-PSO with Binary Search‘ (LPBS) algorithm for discovering motifs, especially species specific motifs.In this study, fragments of mitochondrial cytochrome C oxidase subunit I (COI/COX1) and genome of COI were collected from the Genbank online database.For the first experiment, the genome of COI was used as a reference set and other DNA sequences were used as a comparison set.All the collected DNA sequences are from the same species.The results show that the LPBS algorithm is able to discover motifs. For the second experiment, all the discovered motifs were used as a reference set and the genome of COI from other species were used as a comparison set.The results show that the LPBS algorithm is able to identify correct motifs for species identification.

Item Type: Conference or Workshop Item (Paper)
Additional Information: ISBN: 9789832078791 Organized by: Universiti Utara Malaysia
Uncontrolled Keywords: Particle Swarm Optimization, Linear-PSO, motif discovery, species specific
Subjects: Q Science > QA Mathematics > QA76 Computer software
Divisions: College of Arts and Sciences
Depositing User: Mr. Hazaruddin Harun
Date Deposited: 24 Aug 2014 02:28
Last Modified: 08 Apr 2015 02:13
URI: http://repo.uum.edu.my/id/eprint/11968

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