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An Algorithm for Testing Structure Freeness of Biomolecular Sequences

  • Satoshi Kobayashi
  • Takashi Yokomori
  • Yasubumi Sakakibara
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2950)

Abstract

We are concerned with a problem of checking the structure freeness of S  +  for a given set S of DNA sequences. It is still open whether or not there exists an efficient algorithm for this problem. In this paper, we will give an efficient algorithm to check the structure freeness of S  +  under the constraint that every sequence may form only linear secondary structures, which partially solves the open problem.

Keywords

Minimum Free Energy Loop Length Structure String Unpaired Basis Structure Freeness 
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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Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Satoshi Kobayashi
    • 1
  • Takashi Yokomori
    • 2
  • Yasubumi Sakakibara
    • 3
  1. 1.Dept. of Computer ScienceUniv. of Electro-CommunicationsYokohamaJapan
  2. 2.Dept. of Mathematics, CREST, JST (Japan Science and Technology Corporation), School of EducationWaseda UniversityTokyoJapan
  3. 3.Dept. of Biosciences and Informatics, CREST, JST (Japan Science and Technology Corporation)Keio UniversityChofuJapan

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