Abstract
We investigate the problem of encoding arbitrary data into the words of a DNA language that is defined via the subword closure operation, which appears to be useful in various situations related to data encodings. We present a few theoretical results on the subword closure operation as well as an initial implementation of a web-system that computes DNA languages according to the user’s parameters, and performs encodings of data into these languages.
Research supported by NSERC.
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References
Chen, J., Reif, J.H. (eds.): DNA Computing. LNCS, vol. 2943. Springer, Heidelberg (2004)
Cui, B.: Encoding methods for DNA languages. MSc Thesis, Dept. Math. and Computing Science, Saint Mary’s University, Halifax, Canada (2007)
Ferretti, C., Mauri, G., Zandron, C. (eds.): DNA Computing. LNCS, vol. 3384, pp. 7–10. Springer, Heidelberg (2005)
Grail+: Department of Computer Science. University of Western Ontario, London, Canada. http://www.csd.uwo.ca/Research/grail/
Hagiya, M., Ohuchi, A. (eds.): DNA Computing. LNCS, vol. 2568. Springer, Heidelberg (2003)
Jonoska, N., Mahalingam, K.: Languages of DNA based code words. In: \(\cite{dna9}\), 58–68.
Jonoska, N., Seeman, N.C. (eds.): DNA Computing. LNCS, vol. 2340. Springer, Heidelberg (2002)
Kari, L., Kitto, R., Thierrin, G.: Codes, involutions and DNA encoding. In: Brauer, W., Ehrig, H., Karhumäki, J., Salomaa, A. (eds.) Formal and Natural Computing. LNCS, vol. 2300, pp. 376–393. Springer, Heidelberg (2002)
Kari, L., Konstantinidis, S.: Descriptional complexity of error/edit systems. Journal of Automata, Languages and Combinatorics 9(2/3), 293–309 (2004)
Kari, L., Konstantinidis, S., Sosík, P.: Bond-free languages: formalizations, maximality and construction methods. Intern. Journal of Foundations of Computer Science 16 (2005) 5, 1039–1070. (Conference version in [3], 169–181)
Kobayashi, S., Kondo, T., Arita, M.: On template method for DNA sequence design. In: [5], pp. 205–214
Mahalingam, K.: Involution codes: With application to DNA strand design. PhD Thesis, Dept. Mathematics, University of South Florida, Florida, USA (2004)
Mauri, G., Ferretti, C.: Word Design for Molecular Computing: A Survey. In: [1], pp. 37–46
Tanaka, F., Nakatsugawa, M., Yamamoto, M., Shiba, T., Ohuchi, A.: Developing support system for sequence design in DNA computing. In: [7], pp. 129–137
Yu, S.: Regular Languages. In: Rozenberg, G., Salomaa, A. (eds.) Handbook of Formal Languages, vol. 1, pp. 41–110. Springer, Berlin (1997)
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Cui, B., Konstantinidis, S. (2008). DNA Coding Using the Subword Closure Operation. In: Garzon, M.H., Yan, H. (eds) DNA Computing. DNA 2007. Lecture Notes in Computer Science, vol 4848. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77962-9_30
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DOI: https://doi.org/10.1007/978-3-540-77962-9_30
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-77961-2
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