Abstract
The design of DNA sequences is one of the most practical and important research topics in DNA computing. Although the design of DNA sequences is dependent on the protocol of biological experiments, it is highly required to establish a method for the systematic design of DNA sequences, which could be applied to various design constraints. Recently, Arita proposed an interesting design method, called template method, for DNA word design. The current paper discusses on some extensions of the template method, where we propose a variant of template method, the use of multiple templates, and show their effectiveness. Furthermore, we also present some theoretical properties of templates.
The first author was supported in part by Japan Society for the Promotion of Science, Grant-in-Aid for Exploratory Research NO.13878054, 2001.
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References
L. Adleman, Molecular Computation of Solutions to Combinatorial Problems. Science 266, pp.1021–1024, 1994.
M. Arita and S. Kobayashi, DNA Sequence Design Using Templates, New Generation Computing, 20, pp.263–277, 2002.
A. Ben-Dor, R. Karp, B. Schwikowski, and Z. Yakhini, Universal DNA Tag Systems: A Combinatorial Design Scheme, Proc. of the 4th Annual International Conference on Computational Molecular Biology (RECOMB2000), pp.65–75, 2000.
A.E. Brouwer, J.B. Shearer, N.J.A. Sloane, and W.D. Smith, A New Table of Constant Weight Codes, IEEE Trans. on Information Theory, 36, pp.1334–1380, 1990.
R. Deaton, M. Garzon, J.A. Roze, D.R. Franceschetti, R.C. Murphy and S.E. Jr. Stevens, Reliability and Efficiency of a DNA Based Computation, Physical Review Letter, 80, pp.417–420, 1998.
A. G. Frutos, Q. Liu, A. J. Thiel, A. M.W. Sanner, A. E. Condon, L. M. Smith and R. M. Corn, Demonstration of A Word Design Strategy for DNA Computing on Surfaces, Nucleic Acids Research, Vol.25, No.23, pp.4748–4757, 1997.
M. Garzon, P. Neathery, P. Deaton, R.C. Murphy, D.R. Franceschetti, and S.E. Jr. Stevens, A New Metric for DNA Computing, In Proc. of 2nd Annual Genetic Programming Conference, Morgan Kaufmann, pp.472–478, 1997.
E. J. MacWilliams and N.J.A. Sloane, The Theory of Error-Correcting Codes, North-Holland, 1977.
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Kobayashi, S., Kondo, T., Arita, M. (2003). On Template Method for DNA Sequence Design. In: Hagiya, M., Ohuchi, A. (eds) DNA Computing. DNA 2002. Lecture Notes in Computer Science, vol 2568. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-36440-4_18
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DOI: https://doi.org/10.1007/3-540-36440-4_18
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