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A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences

M. Othman, Razib and Deris, Safaai and Md. IIlias, Rosli (2008) A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences. Journal of Biomedical Informatics , 41 (1). pp. 65-81. ISSN 1532-0464

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Official URL: http://dx.doi.org/10.1016/j.jbi.2007.05.010

Abstract

A genetic similarity algorithm is introduced in this study to find a group of semantically similar Gene Ontology terms. The genetic similarity algorithm combines semantic similarity measure algorithm with parallel genetic algorithm. The semantic similarity measure algorithm is used to compute the similitude strength between the Gene Ontology terms. Then, the parallel genetic algorithm is employed to perform batch retrieval and to accelerate the search in large search space of the Gene Ontology graph. The genetic similarity algorithm is implemented in the Gene Ontology browser named basic UTMGO to overcome the weaknesses of the existing Gene Ontology browsers which use a conventional approach based on keyword matching. To show the applicability of the basic UTMGO, we extend its structure to develop a Gene Ontology -based protein sequence annotation tool named extended UTMGO. The objective of developing the extended UTMGO is to provide a simple and practical tool that is capable of producing better results and requires a reasonable amount of running time with low computing cost specifically for offline usage. The computational results and comparison with other related tools are presented to show the effectiveness of the proposed algorithm and tools.

Item Type:Article
Uncontrolled Keywords:Gene Ontology, genetic algorithm, genetic similarity search, protein sequence annotation, semantic similarity measure
Subjects:T Technology > TP Chemical technology
Divisions:Chemical and Natural Resources Engineering (Formerly known)
ID Code:7281
Deposited By: Maznira Sylvia Azra Mansor
Deposited On:02 Jan 2009 07:00
Last Modified:05 Jan 2011 08:32

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