Universiti Teknologi Malaysia Institutional Repository

Hybridization-ligation versus parallel overlap assembly: an experimental comparison of initial pool generation for direct-proportional length-based DNA computing

Ibrahim, Zuwairie and Tsuboi, Yusei and Ono, Osamu (2006) Hybridization-ligation versus parallel overlap assembly: an experimental comparison of initial pool generation for direct-proportional length-based DNA computing. IEEE Transactions on NanoBioscience , 5 (2). pp. 103-109. ISSN 1536-1241

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Official URL: http://dx.doi.org/10.1109/TNB.2006.875043

Abstract

Previously, direct-proportional length-based DNA computing (DPLB-DNAC) for solving weighted graph problems has been reported. The proposed DPLB-DNAC has been successfully applied to solve the shortest path problem, which is an instance of weighted graph problems. The design and development of DPLB-DNAC is important in order to extend the capability of DNA computing for solving numerical optimization problem. According to DPLB-DNAC, after the initial pool generation, the initial solution is subjected to amplification by polymerase chain reaction and, finally, the output of the computation is visualized by gel electrophoresis. In this paper, however, we give more attention to the initial pool generation of DPLB-DNAC. For this purpose, two kinds of initial pool generation methods, which are generally used for solving weighted graph problems, are evaluated. Those methods are hybridization-ligation and parallel overlap assembly (POA). It is found that for DPLB-DNAC, POA is better than that of the hybridization-ligation method, in terms of population size, generation time, material usage, and efficiency, as supported by the results of actual experiments.

Item Type:Article
Uncontrolled Keywords:direct-proportional length-based DNA computing gel electrophoresis generation time hybridization ligation initial pool generation material usage numerical optimization problem parallel overlap assembly polymerase chain reaction population size weighted graph problems
Subjects:T Technology > TK Electrical engineering. Electronics Nuclear engineering
Divisions:Electrical Engineering
ID Code:1881
Deposited By: Dr Zaharuddin Mohamed
Deposited On:16 Mar 2007 07:28
Last Modified:01 Jun 2010 02:59

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