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DNA Sequence Reconstruction Based On Genetic Algorithm

Md. Rafiqul Islam, and Md. Rowshan Shahriar, and Abul Faisal Mohammad Shaheed, (2008) DNA Sequence Reconstruction Based On Genetic Algorithm. Malaysian Journal of Computer Science, 21 (1). pp. 12-23. ISSN 0127-9084

Full text not available from this repository.

Official URL: http://ejum.fsktm.um.edu.my/ArticleInformation.aspx?ArticleID=625

Affiliations

Khulna University, Bangladesh
Khulna University, Bangladesh
Khulna University, Bangladesh

Abstract

It is becoming increasingly important to develop a novel process for determining the letters of our genetic code, known as DNA sequencing. This task is performed by large datasets using the combination of heuristic methods with little mathematical calculation. In this paper, we present a new method for DNA sequence reconstruction using genetic algorithm, which is able to predict the actual DNA sequence. The performance of the genetic algorithm is evaluated with respect to previous methods in the literature. The results indicate that the proposed new method is superior to previous methods. Finally we compare the results of the experiment and discuss the performance of the proposed method in the DNA sequence reconstruction.

Item Type:Journal
Keywords:DNA Sequence, Subsequence, Oligonucleotide, Population Construction, Fitness Function, Crossover, Mutation
Subjects:Q Science, Computer Science
ID Code:2293

[1] Jacek Blazewicz, Fred Glover, Marta Kasprzak. DNA Sequencing-Tabu and Scatter Search Combined. Information Journal on Computing Vol. 16, No. 3, summer 2004, pp. 232-240.

[2] Md. Rafiqul Islam, Md. Shams-Ur Rahim, A. H. M. Saiful Islam and Mr. Shahidul Islam. Reconstruction of a DNA sequence from its Probes in Sequencing by Hybridization. International Conference on Computer and Information Technology (ICCIT), Dhaka, Bangladesh, 2003.

[3] Shyi-Ming Chen*, Chung-Hui Lin, and Shi-Jay Chen. Multiple DNA Sequence Alignment Based on Genetic Algorithms and Divide-and-Conquer Techniques. International Journal of Applied Science and Engineering, 2005. 3, 2: 89-100.

[4] Md. Kamruzzaman, Sk. Mamunur Rashid, Arpita Majumder. DNA Sequence Reconstruction Using SequenceBy Hybridization Method With Negative And Positive Errors. Undergraduate thesis, CSE Discipline, Khulna University, Khulna, Bangladesh, 2005.

[5] Nicholas M. Hann, Simon J. Godsill. Baysian Models for DNA Sequence. Proceedings of IEEE international conference on acoustics, speech, and signal processing, 2002.0-7803-7402-9/02.

[6] Maria Calvino, Nuria Gomez, Luis F. Mingo. DNA Simulation of Genetic Algorithm: Fitness Computation, International Journal “Information Theories & Application”, Vol. 14 / 2007.

[7] Jacek Blazewicz, Piotr Formanowicz, Frederic Guinand and Marta Kasprzak. A heuristic managing error for DNA sequencing, Journal on bioinformatics vol. 18 no. 5, 2002, Pages 652-660.

[8] www.awl-he.con/biology

[9] Carlos A. Brizuela, Luis C. Gonzalez-Gurrol, Andrei Tchernykh, Denis Trystram, Sequencing by hybridization: an enhanced crossover operator for a hybrid genetic algorithm. J. Heuristics (2007) 13: 209–225.

[10] Jacek Blazewicz, Ceyda Oguz, Aleksandra Swiercz, DNA Sequencing by Hybridization via Genetic Search, OPERATION RESEARCH Vol.54, No. 6, November-December 2006, pp. 1185-1192.

[11] Jacek Blazewicz, Marta Kasprzakl, and Wojciech Kuroczycki, Hybrid Genetic Algorithm for DNA Sequencing with Errors, Journal of Heuristics, Vol. Number 5/ September, 2002, 495-502.

[12] J. Dylan Spalding, Cara MacNish, A Genetic Algorithm to Sequence DNA using Sequencing by Hybridization Experimental Data, Journal of Heuristics, 0-7803-7804-0/03/ 2003.

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