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A Formal Model for Databases in DNA

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Algebraic and Numeric Biology

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6479))

Abstract

Our goal is to better understand, at a theoretical level, the database aspects of DNA computing. Thereto, we introduce a formally defined data model of so-called sticker DNA complexes, suitable for the representation and manipulation of structured data in DNA. We also define DNAQL, a restricted programming language over sticker DNA complexes. DNAQL stands to general DNA computing as the standard relational algebra for relational databases stands to general-purpose conventional computing. The number of operations performed during the execution of a DNAQL program, on any input, is only polynomial in the dimension of the data, i.e., the number of bits needed to represent a single data entry. Moreover, each operation can be implemented in DNA using a constant number of laboratory steps. We prove that the relational algebra can be simulated in DNAQL.

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Author information

Authors and Affiliations

  1. Hasselt University and Transnational University of Limburg, Agoralaan Gebouw D, 3590, Diepenbeek, Belgium

    Joris J. M. Gillis & Jan Van den Bussche

Authors
  1. Joris J. M. Gillis
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  2. Jan Van den Bussche
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Editor information

Editors and Affiliations

  1. Computational Biology Research Centre (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 135-0064, Tokyo, Japan

    Katsuhisa Horimoto

  2. Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology, 135-0064, Tokyo, Japan

    Masahiko Nakatsui

  3. Research Institute for Symbolic Computation(RISC), Johannes Kepler University of Linz, 4040, Linz, Austria

    Nikolaj Popov

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Gillis, J.J.M., Van den Bussche, J. (2012). A Formal Model for Databases in DNA. In: Horimoto, K., Nakatsui, M., Popov, N. (eds) Algebraic and Numeric Biology. Lecture Notes in Computer Science, vol 6479. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28067-2_2

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  • DOI: https://doi.org/10.1007/978-3-642-28067-2_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-28066-5

  • Online ISBN: 978-3-642-28067-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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