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DNA has certain unique properties such as self-assembly and self-complementary in hybridization, which are important in many DNA-based technologies. DNA computing, for example, uses these properties to realize a computation, in vitro, which consists of several chemical reactions [1]. Other DNA-based technologies such as DNA chips for mutational analysis and sequencing [2] also depend on hybridization to assemble nanostructure and to amplify DNA templates, respectively. Hybridization of DNA can be controlled by properly designing DNA sequences.
A number of DNA sequence design methodologies have been proposed to date [3-9]. Recently, Ant Colony System (ACS) has been employed in DNA sequence design [10]. Based on this approach, DNA sequence design problem is modeled, similar to a finite state machine of four nodes, as a path-finding problem. Since the DNA sequence design problem offers no information which can be directly used as heuristic information, this model only uses pheromone information for ACO computations.
ACS, however, commonly requires heuristic information in the computation. Hence, there is a need to investigate some DNA parameters to improve the stochastic search of ACS for DNA sequence design. In fact, in DNA studies, there are some nearest-neighbor thermodynamic parameters, which are commonly used in calculating melting temperature of double-stranded DNAs.
In this research proposal, similar objective functions and constraints from [10] will be used. Two objective functions, namely Hmeasure and similarity, are chosen to estimate the uniqueness of each DNA sequence. Moreover, two additional objective functions, which are hairpin and continuity, will be used in order to avoid a secondary structure of a DNA sequence. Furthermore, two constraints, which are GCcontent and melting temperature, are used to maintain uniform chemical characteristics of DNA. Thus, it is expected that the nearest-neighbor parameter will provide positive contributions to the stochastic search based on ACS algorithm in DNA sequence design.
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