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DNASequenceGenerator: A Program for the Construction of DNA Sequences

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DNA Computing (DNA 2001)

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

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Abstract

In DNA Computing and DNA nanotechnology the design of proper DNA sequences turned out to be an elementary problem [1, 2, 3, 4, 5, 6, 7, 8, 9]. We here present a software program for the construction of sets (“pools”) of DNA sequences. The program can create DNA sequences to meet logical and physical parameters such as uniqueness, melting temperature and GC ratio as required by the user. It can create sequences de novo, complete sequences with gaps and allows import and recycling of sequences that are still in use. The program always creates sequences that are — in terms of uniqueness, GC ratio and melting temperature — “compatible” to those already in the pool, no matter whether those were added manually or created or completed by the program itself. The software comes with a GUI and a Sequence Wizard. In vitro tests of the program’s output were done by generating a set of oligomers designed for self-assembly. The software is available for download under http://LS11-www.cs.uni-dortmund.de/molcomp/Downloads/downloads. html.

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Author information

Authors and Affiliations

  1. Chair of System Analysis, University of Dortmund, Germany

    Udo Feldkamp, Wolfgang Banzhaf & Hilmar Rauhe

  2. Institute of Genetics, University of Cologne, Germany

    Sam Saghafi

Authors
  1. Udo Feldkamp
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  2. Sam Saghafi
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  3. Wolfgang Banzhaf
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  4. Hilmar Rauhe
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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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Feldkamp, U., Saghafi, S., Banzhaf, W., Rauhe, H. (2002). DNASequenceGenerator: A Program for the Construction of DNA Sequences. 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_3

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  • DOI: https://doi.org/10.1007/3-540-48017-X_3

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  • 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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