A simulation software for DNA computing algorithms implementation

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The capturing of gel electrophoresis image represents the output of a DNA computing algorithm. Before this image is being captured, DNA computing involves parallel overlap assembly (POA) and polymerase chain reaction (PCR) that is the main of this computing algorithm. However, the design of the DNA oligonucleotides to represent a problem is quite complicated and is prone to errors. In order to reduce these errors during the design stage before the actual in-vitro experiment is carried out; a simulation software capable of simulating the POA and PCR processes is developed. This simulation software capability is unlimited where problem of any size and complexity can be simulated, thus saving cost due to possible errors during the design process. Information regarding the DNA sequence during the computing process as well as the computing output can be extracted at the same time using the simulation software.

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... In [35] a simulation software for the DNA computing algorithm in [1] is proposed. In [36] a simulation software for the DNA computing solution of the elevator scheduling problem is proposed. ...
... Another group of works is devoted to the development of these methods. For example, the works of J. Pizzonia [15] and L. Carol [16], GILE software (Gel-Image-Extractor) [17] or [18][19][20][21][22][23]. In [18], gels in large scale were analysed, [19] used the method of least squares, and [20] shows a method of using morphological operations (erosion) in the analysis of ROI (Region Of Interest) of gels. ...
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The analysis of polyacrylamide gels is currently carried out manually or automatically. In the automatic method, there are limitations related to the acceptable degree of distortion of lane and band continuity. The available software cannot deal satisfactorily with this type of situations. Therefore, the paper presents an original image analysis method devoid of the aforementioned drawbacks. Material: This paper examines polyacrylamide gel images from Li-Cor DNA Sequencer 4300S resulting from the use of the electrophoretic separation of DNA fragments. The acquired images have a resolution dependent on the length of the analysed DNA fragments and typically it is MGxNG=3806x1027 pixels. The images are saved in TIFF format with a grayscale resolution of 16 bits/pixel. The presented image analysis method was performed on gel images resulting from the analysis of DNA methylome profiling in plants exposed to drought stress, carried out with the MSAP (Methylation Sensitive Amplification Polymorphism) technique. The results of DNA polymorphism analysis were obtained in less than one second for the Intel CoreTM 2 Quad CPU Q9300@2.5GHz, 8GB RAM. In comparison with other known methods, specificity was 0.95, sensitivity = 0.94 and AUC (Area Under Curve) = 0.98. It is possible to carry out this method of DNA polymorphism analysis on distorted images of polyacrylamide gels. The method is fully automatic and does not require any operator intervention. Compared with other methods, it produces the best results and the resulting image is easy to interpret. The presented method of measurement is used in the practical analysis of polyacrylamide gels in the Department of Genetics at the University of Silesia in Katowice, Poland.
Conference Paper
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We propose an encoding method of numerical data in DNA using temperature gradient. We introduce melting temperature (Tm) for this purpose. Melting temperature is a unique characteristic to ma- nipulate the hybridization and denaturation processes that used in the key steps in DNA computing such as the solution generation step and the amplification step. DNA strands of lower melting temperature tend to denature with ease and also be easily amplified by slightly modi- fied polymerase chain reaction, called denaturation temperature gradi- ent polymerase chain reaction. Using these properties, we implement a local search molecular algorithm using temperature gradient, which is contrasted to conventional exhaustive search molecular algorithms. The proposed methods are verified by solving an instance of the travelling salesman problem. We could effectively amplify the correct solution and the use of temperature gradient made the detection of solutions easier.
Conference Paper
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Most DNA-computing algorithms to solve mathematical problems start with combinatorial generation of an initial pool. Several methods for initial-pool generation have been proposed, including hybridization/ligation, parallel overlap assembly, and mix/split. Here we implement and compare the hybridization/ligation method by Adleman and the parallel overlap assembly method by Stemmer, both introduced in 1994. We apply these methods to the molecular algorithm by Kaplan et al. in 1997 to solve a weighted graph problem. Our experimental results support that parallel overlap assembly is a better choice in terms of generation speed and material consumption than the hybridization/ligation-based method.
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Deoxyribonucleic Acid or DNA computing has emerged as an interdisciplinary field that draws together chemistry, molecular biology, computer science, and mathematics. From the DNA computing point of view, it has been proven that it is possible to solve weighted graph problems by exploiting some characteristics of DNA such as length, concentration, and melting temperature. In this paper, we present an alternative direct-proportional length-based DNA computing approach whereby the cost of each path is encoded by the length of the oligonucleotides in a proportional way. The advantage is such that, after the hybridization and ligation reactions, gel electrophoresis can be performed to separate the respective DNA duplex according to their length which directly decodes the results. In addition to this advantage, the reliability of the proposed approach can be enhanced as only the general and well-known bio-molecular laboratory operations are employed during the computation.
Conference Paper
Implementation and experimental procedures to solve an elevator scheduling problem using direct-proportional length-based DNA computing approach are presented in this paper. All possible travel path combinations of the elevators are encoded by oligonucleotides of length directly proportional to the elevators traveling time based on certain initial conditions such as elevators present and destination floors, and hall calls from a floor. Parallel overlap assembly is employed for initial pool generation and polymerase chain reaction for amplification. Gel electrophoresis is then performed to separate all the generated travel paths by its oligonucleotides lengths. The gel electrophoresis image is then captured to visualize the required optimal path. Experimental result shows that DNA computing approach can be well-suited for solving such real-world problem of this type of nature.
Concentration-controlled DNA computing is presented for accomplishing a local search for the solution of a shortest path problem. In this method, the concentrations of DNA representing edges are determined according to the costs on edges, and then the hybridization process is performed. Since the concentrations of hopeless candidate solutions tend to be small after the hybridization process, a local search by concentration-controlled DNA computing is a promising approach. In order to discuss about the relationship between given costs on edges in the graph and concentrations of generated DNA paths, a simulation model of the hybridization process is used and the results of a laboratory experiment are shown.
Algorithms for computing with DNA currently require the construction of pools of molecules in which each distinct molecule represents a different starting point for the calculation. We have begun building such pools using the technique of parallel overlap assembly that is already used for the generation of diversity in biologically useful combinatorial search techniques such as gene shuffling. Unlike these applications, a pool in a molecular computer must be complete, containing all possible strands, and ordered, having minimal contamination from incorrectly assembled DNA. We present an experiment in which parallel overlap assembly is used to construct a computational pool and an experiment in which this pool is used to solve the NP-complete maximal-clique problem.
The tools of molecular biology were used to solve an instance of the directed Hamiltonian path problem. A small graph was encoded in molecules of DNA, and the "operations" of the computation were performed with standard protocols and enzymes. This experiment demonstrates the feasibility of carrying out computations at the molecular level.
Temperature gradient-based DNA computing for graph problems with weighted edges
  • J Y Lee
  • S Y Shin
  • S J Augh
  • T H Park
  • B T Zhang
J.Y. Lee, S.Y. Shin, S.J. Augh, T.H. Park and B.T. Zhang, "Temperature gradient-based DNA computing for graph problems with weighted edges," Lecture Notes in Computer Science, 2568, pp 73-84 (2003).
DNA sequence generator: A program for the construction of DNA sequences
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F. Udo, S. Sam, B. Wolfgang and R. Hilmar, "DNA sequence generator: A program for the construction of DNA sequences," Proceedings of the Seventh International Workshop on DNA Based Computers, Florida, pp 23-32 (2001).
Engineering Introduction to Biotechnology
  • J P Fitch
J.P. Fitch, Engineering Introduction to Biotechnology, SPIE Press, Washington, (2001).