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International Workshop on DNA-Based Computers

DNA 2001: DNA Computing pp 129–137Cite as

Developing Support System for Sequence Design in DNA Computing

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Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2340))

Abstract

Sequence design is the important factor which governs the reaction of DNA. In related researches, the method to minimize (or maxmize) the evaluation function based on knowledge of sequence design has been used. In this paper, we develop support system for sequence design in DNA computing, which minimizes the evaluation function calculated as the linear sum of the plural evaluation terms. Our system not only searches for good sequences but also presents contribution ratio of each evaluation term to the evaluation function and can reduce the number of combination of evaluation terms by reduction of the evaluation function. It helps us to find a good criteria for sequence design in DNA computing.

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References

  1. Masanori Arita, Akio Nishikawa, Masami Hagiya, Ken Komiya, Hidetaka Gouzu and Kensaku Sakamoto: “Improving Sequence Design for DNA Computing,” Proceedings of GECCO’00 (Genetic and Evolutionary Computation Conference), pp. 875–882 (2000)

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  2. M. Garzon, R. Deaton, L.F. Nino, Ed Stevens: Encoding Genomes for DNA Computing, Proc. of the Third Annual Genetic Programming Conf., pp. 684–690, 1998

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  3. R. Deaton, R. C. Murphy, M. Garzon, D. R. Franceschetti and S. E. Stevens, Jr.: “Good Encodings for DNA-Based Solutions to Combinatorial Problems,” DNA Based Computers II, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Vol. 44, pp. 247–258 (1999)

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  4. JAMES G. WETMUR, “Physical Chemistry of Nucleic Acid Hybridization,” DNA Based Computers III, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Vol. 48, pp. 1–23 (1999)

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Author information

Authors and Affiliations

  1. Division of Systems and Information Eng., Graduate School of Eng., Hokkaido University, Japan

    Fumiaki Tanaka, Masashi Nakatsugawa, Masahito Yamamoto & Azuma Ohuchi1

  2. Division of Molecular Chemistry Eng., Graduate School of Eng., Hokkaido University, Nishi 8, Kita 13, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan

    Toshikazu Shiba

Authors
  1. Fumiaki Tanaka
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  2. Masashi Nakatsugawa
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  3. Masahito Yamamoto
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  4. Toshikazu Shiba
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  5. Azuma Ohuchi1
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Editor information

Editors and Affiliations

  1. Department of Mathematics, University of South Florida, 4202 E. Fowler A. PHY 114, Tampa, FL, 33620, USA

    Nataša Jonoska

  2. Department of Chemistry, New York University, New York, NY, 10003, USA

    Nadrian C. Seeman

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© 2002 Springer-Verlag Berlin Heidelberg

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Cite this paper

Tanaka, F., Nakatsugawa, M., Yamamoto, M., Shiba, T., Ohuchi1, A. (2002). Developing Support System for Sequence Design in DNA Computing. In: Jonoska, N., Seeman, N.C. (eds) DNA Computing. DNA 2001. Lecture Notes in Computer Science, vol 2340. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-48017-X_12

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  • DOI: https://doi.org/10.1007/3-540-48017-X_12

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-43775-8

  • Online ISBN: 978-3-540-48017-4

  • eBook Packages: Springer Book Archive

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