title: Hybridization-ligation versus parallel overlap assembly: an experimental comparison of initial pool generation for direct-proportional length-based DNA computing.
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.
authors.affiliation: Department of Mechatronics and Robotics, Faculty of Electrical Engineering, Universiti Teknologi Malaysia, 81310 UTM Skudai, Malaysia. zuwairie@ieee.org
authors.forename: Zuwairie
authors.initials: Z
authors.lastname: Ibrahim
authors.forename: Yusei
authors.initials: Y
authors.lastname: Tsuboi
authors.forename: Osamu
authors.initials: O
authors.lastname: Ono
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D039301:Computers, Molecular; D004247:DNA / Q000032:analysis* / Q000737:chemistry* / Q000235:genetics; D005788:Gene Pool; D008956:Models, Chemical; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA