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

  • Atsushi Kijima
  • Satoshi Kobayashi
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3892)


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.


Minimum Free Energy Regular Language Loop Length Stochastic Local Search Structure String 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Atsushi Kijima
    • 1
  • Satoshi Kobayashi
    • 1
  1. 1.Graduate School of University of Electro-CommunicationsTokyoJapan

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