A filtering algorithm for efficient retrieving of DNA sequence

DNA sequence similarity search is an important task in computational biology applications. Similarity search procedure is executed by an alignment process between query and targeted sequences. An optimal alignment process based on the dynamic programming algorithms has shown to have O(n m) time and...

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Main Authors:	Abdul Rahman, Mohd Nordin, Mohd. Saman, Md. Yazid, Ahmad, Aziz, Md. Tap, Abu Osman
Format:	Article
Language:	English
Published:	International Association of Computer Science and Information Technology Press (IACSIT) 2009
Subjects:	T Technology (General) TK7885 Computer engineering
Online Access:	http://irep.iium.edu.my/1205/ http://irep.iium.edu.my/1205/ http://irep.iium.edu.my/1205/1/A_Filtering_Algorithm_For_Efficient_Retrieving_of_DNA_Sequence.pdf

id	iium-1205
recordtype	eprints
spelling	iium-12052012-03-20T08:26:17Z http://irep.iium.edu.my/1205/ A filtering algorithm for efficient retrieving of DNA sequence Abdul Rahman, Mohd Nordin Mohd. Saman, Md. Yazid Ahmad, Aziz Md. Tap, Abu Osman T Technology (General) TK7885 Computer engineering DNA sequence similarity search is an important task in computational biology applications. Similarity search procedure is executed by an alignment process between query and targeted sequences. An optimal alignment process based on the dynamic programming algorithms has shown to have O(n m) time and space complexity. Heuristics algorithms can process a fast DNA sequence alignment, but generate low comparison sensitivity. The biologists frequently demand for optimal comparison result so that the perfect structure of living beings evolution can be constructed. This task becomes more complex and challenging as the sizes of public sequence databases get very large and are increasing exponentially each year. The aim of this study is to develop a filtering algorithm in order to reduce the iteration of dynamic programming process and therefore an efficient process of retrieving a set of similar DNA sequences in database can be made. The algorithm filtered the expected irrelevant DNA sequences in database from being computed for dynamic programming based optimal alignment process. An automaton-based algorithm is used to develop the filtering process proposed. A set of random patterns is generated from query sequence are placed in automaton machine before exact matching and scoring process is performed. Extensive experiments have been carried out on several parameters and the results show that the developed filtering algorithm removed the unrelated targeted sequences from being aligned with query sequence International Association of Computer Science and Information Technology Press (IACSIT) 2009-06 Article PeerReviewed application/pdf en http://irep.iium.edu.my/1205/1/A_Filtering_Algorithm_For_Efficient_Retrieving_of_DNA_Sequence.pdf Abdul Rahman, Mohd Nordin and Mohd. Saman, Md. Yazid and Ahmad, Aziz and Md. Tap, Abu Osman (2009) A filtering algorithm for efficient retrieving of DNA sequence. International Journal of Computer Theory and Engineering, 1 (2). pp. 102-109. ISSN 1793-821X (O), 1793-8201 (P) http://www.ijcte.org/abstract/016.htm
repository_type	Digital Repository
institution_category	Local University
institution	International Islamic University Malaysia
building	IIUM Repository
collection	Online Access
language	English
topic	T Technology (General) TK7885 Computer engineering
spellingShingle	T Technology (General) TK7885 Computer engineering Abdul Rahman, Mohd Nordin Mohd. Saman, Md. Yazid Ahmad, Aziz Md. Tap, Abu Osman A filtering algorithm for efficient retrieving of DNA sequence
description	DNA sequence similarity search is an important task in computational biology applications. Similarity search procedure is executed by an alignment process between query and targeted sequences. An optimal alignment process based on the dynamic programming algorithms has shown to have O(n m) time and space complexity. Heuristics algorithms can process a fast DNA sequence alignment, but generate low comparison sensitivity. The biologists frequently demand for optimal comparison result so that the perfect structure of living beings evolution can be constructed. This task becomes more complex and challenging as the sizes of public sequence databases get very large and are increasing exponentially each year. The aim of this study is to develop a filtering algorithm in order to reduce the iteration of dynamic programming process and therefore an efficient process of retrieving a set of similar DNA sequences in database can be made. The algorithm filtered the expected irrelevant DNA sequences in database from being computed for dynamic programming based optimal alignment process. An automaton-based algorithm is used to develop the filtering process proposed. A set of random patterns is generated from query sequence are placed in automaton machine before exact matching and scoring process is performed. Extensive experiments have been carried out on several parameters and the results show that the developed filtering algorithm removed the unrelated targeted sequences from being aligned with query sequence
format	Article
author	Abdul Rahman, Mohd Nordin Mohd. Saman, Md. Yazid Ahmad, Aziz Md. Tap, Abu Osman
author_facet	Abdul Rahman, Mohd Nordin Mohd. Saman, Md. Yazid Ahmad, Aziz Md. Tap, Abu Osman
author_sort	Abdul Rahman, Mohd Nordin
title	A filtering algorithm for efficient retrieving of DNA sequence
title_short	A filtering algorithm for efficient retrieving of DNA sequence
title_full	A filtering algorithm for efficient retrieving of DNA sequence
title_fullStr	A filtering algorithm for efficient retrieving of DNA sequence
title_full_unstemmed	A filtering algorithm for efficient retrieving of DNA sequence
title_sort	filtering algorithm for efficient retrieving of dna sequence
publisher	International Association of Computer Science and Information Technology Press (IACSIT)
publishDate	2009
url	http://irep.iium.edu.my/1205/ http://irep.iium.edu.my/1205/ http://irep.iium.edu.my/1205/1/A_Filtering_Algorithm_For_Efficient_Retrieving_of_DNA_Sequence.pdf
first_indexed	2023-09-18T20:08:24Z
last_indexed	2023-09-18T20:08:24Z
_version_	1777407313494147072

A filtering algorithm for efficient retrieving of DNA sequence

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