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Identifying the definite base of COI for extraction of DNA sequences using LPBS


Syed Abdullah, Sharifah Lailee and Harun, Hazaruddin and Mohd Hussin, Naimah and Hamid, Jiwa Noris and Mohamed Hanaphi, Roziana (2012) Identifying the definite base of COI for extraction of DNA sequences using LPBS. In: 2012 IEEE Symposium on Humanities, Science and Engineering Research (SHUSER), 24-27 June 2012, Kuala Lumpur.

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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, two samples from different fragments of `mitochondrial cytochrome C oxidase subunit I' (COI/COX1) were collected from the Genbank online database.DNA sequences for the first sample are a mix of different fragments of COI and the second sample is from the same fragment of COI.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 of greater length when using DNA sequences from the same fragment of COI.The experiment also found that 139 can be used as a starting base for COI DNA sequences extraction to discover species-specific motifs.

Item Type: Conference or Workshop Item (Paper)
Uncontrolled Keywords: Particle Swarm Optimization; Linear-PSO; motif discovery; species specific
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Divisions: School of Computing
Depositing User: Mr. Hazaruddin Harun
Date Deposited: 18 Jan 2017 03:18
Last Modified: 18 Jan 2017 03:18
URI: http://repo.uum.edu.my/id/eprint/20639

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