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DNA Sequence Design by Dynamic Neighborhood Searches

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DNA Computing (DNA 2006)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4287))

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Abstract

We propose a local-search based algorithm to design DNA sequence sets that satisfy several combinatorial constraints about hamming-distance criteria. To deal with the constraints in the local search, we adopt elaborate (and dynamic) neighborhood search frameworks called the Variable Neighborhood Search (VNS) and the Variable Depth Search (VDS). Although our algorithm can deal with many types of hamming distance-based constraints and is easy to extend (e.g., also applicable for other constraints), in computational experiments, we succeeded in generating better sequence sets than the ones generated by exiting methods of more specified constraints.

This research partly received financial support from Scientific research fund of Ministry of Education, Culture, Sports, Science and Technology.

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Author information

Authors and Affiliations

  1. Dept. of Computer Science and Communication Engineering, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka, 812-8581, Japan

    Suguru Kawashimo, Hirotaka Ono, Kunihiko Sadakane & Masafumi Yamashita

Authors
  1. Suguru Kawashimo
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  2. Hirotaka Ono
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  3. Kunihiko Sadakane
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  4. Masafumi Yamashita
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Editor information

Editors and Affiliations

  1. Department of Chemistry, Purdue University, 560 Oval Drive, 47907-2084, West Lafayette, IN, USA

    Chengde Mao

  2. Faculty of Education and Integrated Arts and Sciences, Department of Mathematics, Waseda University, 1-6-1 Nishiwaseda, Shinjuku-ku, 169-8050, Tokyo, Japan

    Takashi Yokomori

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© 2006 Springer-Verlag Berlin Heidelberg

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Kawashimo, S., Ono, H., Sadakane, K., Yamashita, M. (2006). DNA Sequence Design by Dynamic Neighborhood Searches. In: Mao, C., Yokomori, T. (eds) DNA Computing. DNA 2006. Lecture Notes in Computer Science, vol 4287. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11925903_12

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  • DOI: https://doi.org/10.1007/11925903_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-49024-1

  • Online ISBN: 978-3-540-68423-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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