A Simulation Software for DNA Computing Algorithms Implementation
Commenced in January 2007
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A Simulation Software for DNA Computing Algorithms Implementation

Authors: M. S. Muhammad, S. M. W. Masra, K. Kipli, N. Zamhari


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.

Keywords: DNA computing, PCR, POA, simulation software

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1334393

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[1] L.M. Adleman, "Molecular computation of solutions to combinatorial problems," Science, 266, pp 1021-1024 (1994).
[2] Z. Ibrahim, Y. Tsuboi, O. Ono and M. Khalid, "Direct-proportional length-based DNA computing for shortest path problem," International Journal of Computer Science and Applications, 1(1), pp 46-60 (2004).
[3] 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).
[4] Y. Yamamoto, A. Kameda, N. Matsuura, T. Shiba, Y. Kawazoe and A. Ahochi, "Local search by concentration-controlled DNA computing," International Journal of Computational Intelligence and Applications, 2, pp 447-455 (2002).
[5] M.S. Muhammad, Z. Ibrahim, O. Ono and M. Khalid, "Directproportional length-based DNA computing implementation for elevator scheduling problem", Proceedings of the IEEE International Region 10 Conference (TENCON2005), Melbourne, pp 711-715 (2005).
[6] 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).
[7] P.D. Kaplan, Q. Ouyang, D.S. Thaler and A. Libchaber, "Parallel overlap assembly for the construction of computational DNA libraries," Journal of Theoretical Biology, 188(3), pp 333-341 (1997).
[8] J.Y. Lee, H.W. Lim, S.I. Yoo, B.T. Zhang and T.H. Park, "Efficient initial pool generation for weighted graph problems using parallel overlap assembly," Proceedings of the 10th International Meeting on DNA Computing, Milan, pp 357-364 (2004).
[9] J.P. Fitch, Engineering Introduction to Biotechnology, SPIE Press, Washington, (2001).
[10] G. Paun, G. Rozenberg and A. Salomaa, "DNA computing: new computing paradigms," Lecture Notes in Computer Science, 1644, pp 106-118 (1998).