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Linear-PSO with binary search algorithm for DNA Motif Discovery / Hazaruddin Harun

Motif Discovery (MD) is the process of identifying meaningful patterns in DNA, RNA, or protein sequences. In the field of bioinformatics, a pattern is also known as a motif. Numerous algorithms had been developed for MD, but most of these were not designed to discover species specific motifs used in...

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Main Author: Harun, Hazaruddin
Format: Book Section
Language:English
Published: Institute of Graduate Studies, UiTM 2015
Subjects:
Malaysia
Online Access:http://ir.uitm.edu.my/id/eprint/19220/1/ABS_HAZARUDDIN%20HARUN%20TDRA%20VOL%207%20IGS%2015.pdf
http://ir.uitm.edu.my/id/eprint/19220/
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spelling my.uitm.ir.192202018-06-12T06:53:21Z http://ir.uitm.edu.my/id/eprint/19220/ Linear-PSO with binary search algorithm for DNA Motif Discovery / Hazaruddin Harun Harun, Hazaruddin Malaysia Motif Discovery (MD) is the process of identifying meaningful patterns in DNA, RNA, or protein sequences. In the field of bioinformatics, a pattern is also known as a motif. Numerous algorithms had been developed for MD, but most of these were not designed to discover species specific motifs used in identifying a specifically selected species where the exact location of these motifs also needs to be identified. Evaluation of these algorithms showed that the results are unsatisfactory due to the lower validity and accuracy of these algorithms. At present, DNA sequencing analysis is the most utilised technique for species identification where patterns of DNA sequences are determined by comparing the sequence to comprehensive databases. However, several false and gap sequences had been identified to be present in these databases which lead to false identification. Therefore, this study addresses these problems by introducing a hybrid algorithm for MD. In this study, the MD is a process to discover all possible motifs that existed in DNA sequences whereas Motif Identification (MI) is a process to identify the correct motif that can represent a selected species. Particle Swarm Optimisation (PSO) was selected as the base algorithm that needs improvement and integration with other techniques. The Linear-PSO algorithm was the first version of improvement… Institute of Graduate Studies, UiTM 2015 Book Section PeerReviewed text en http://ir.uitm.edu.my/id/eprint/19220/1/ABS_HAZARUDDIN%20HARUN%20TDRA%20VOL%207%20IGS%2015.pdf Harun, Hazaruddin (2015) Linear-PSO with binary search algorithm for DNA Motif Discovery / Hazaruddin Harun. In: The Doctoral Research Abstracts. IPSis Biannual Publication, 7 (7). Institute of Graduate Studies, UiTM.
institution Universiti Teknologi Mara
building Tun Abdul Razak Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Teknologi Mara
content_source UiTM Institutional Repository
url_provider http://ir.uitm.edu.my/
language English
topic Malaysia
spellingShingle Malaysia
Harun, Hazaruddin
Linear-PSO with binary search algorithm for DNA Motif Discovery / Hazaruddin Harun
description Motif Discovery (MD) is the process of identifying meaningful patterns in DNA, RNA, or protein sequences. In the field of bioinformatics, a pattern is also known as a motif. Numerous algorithms had been developed for MD, but most of these were not designed to discover species specific motifs used in identifying a specifically selected species where the exact location of these motifs also needs to be identified. Evaluation of these algorithms showed that the results are unsatisfactory due to the lower validity and accuracy of these algorithms. At present, DNA sequencing analysis is the most utilised technique for species identification where patterns of DNA sequences are determined by comparing the sequence to comprehensive databases. However, several false and gap sequences had been identified to be present in these databases which lead to false identification. Therefore, this study addresses these problems by introducing a hybrid algorithm for MD. In this study, the MD is a process to discover all possible motifs that existed in DNA sequences whereas Motif Identification (MI) is a process to identify the correct motif that can represent a selected species. Particle Swarm Optimisation (PSO) was selected as the base algorithm that needs improvement and integration with other techniques. The Linear-PSO algorithm was the first version of improvement…
format Book Section
author Harun, Hazaruddin
author_facet Harun, Hazaruddin
author_sort Harun, Hazaruddin
title Linear-PSO with binary search algorithm for DNA Motif Discovery / Hazaruddin Harun
title_short Linear-PSO with binary search algorithm for DNA Motif Discovery / Hazaruddin Harun
title_full Linear-PSO with binary search algorithm for DNA Motif Discovery / Hazaruddin Harun
title_fullStr Linear-PSO with binary search algorithm for DNA Motif Discovery / Hazaruddin Harun
title_full_unstemmed Linear-PSO with binary search algorithm for DNA Motif Discovery / Hazaruddin Harun
title_sort linear-pso with binary search algorithm for dna motif discovery / hazaruddin harun
publisher Institute of Graduate Studies, UiTM
publishDate 2015
url http://ir.uitm.edu.my/id/eprint/19220/1/ABS_HAZARUDDIN%20HARUN%20TDRA%20VOL%207%20IGS%2015.pdf
http://ir.uitm.edu.my/id/eprint/19220/
_version_ 1685649183546015744
score 13.222552

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