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Efficient Algorithm for Testing Structure Freeness of Finite Set of Biomolecular Sequences

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DNA Computing (DNA 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3892))

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Abstract

In this paper we will focus on the structure freeness test problem of finite sets of sequences. The result is an extension of Andronescu’s algorithm which can be applied to the sequence design of various DNA computing experiments. We will first give a general algorithm for this problem which runs in O(n 5) time. Then, we will give an evaluation method for sequence design system, which requires O(n 5) time for precomputation, and O(n 4) time and O(n 5) space for each evaluation of sequence sets. The authors believe that this result will give an important progress of efficient sequence design systems.

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Author information

Authors and Affiliations

  1. Graduate School of University of Electro-Communications, 1-5-1, Chofugaoka, Chofu, Tokyo, 182-8585, Japan

    Atsushi Kijima & Satoshi Kobayashi

Authors
  1. Atsushi Kijima
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  2. Satoshi Kobayashi
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Editor information

Editors and Affiliations

  1. Department of Computer Science, Université Pierre et Marie Curie, INSERM U511,, 91 Boulevard de L’Hôpital, 75013, Paris, France

    Alessandra Carbone

  2. California Institute of Technology, Applied and Computational Mathematics, Bioengineering,, MC 114-96, 91125, Pasadena, CA, USA

    Niles A. Pierce

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Kijima, A., Kobayashi, S. (2006). Efficient Algorithm for Testing Structure Freeness of Finite Set of Biomolecular Sequences. In: Carbone, A., Pierce, N.A. (eds) DNA Computing. DNA 2005. Lecture Notes in Computer Science, vol 3892. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11753681_13

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  • DOI: https://doi.org/10.1007/11753681_13

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-34161-1

  • Online ISBN: 978-3-540-34165-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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