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Recognizing DNA Splicing

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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

Motivated by recent techniques developed for observing evolutionary dynamics of a single DNA molecule, we introduce a formal model for accepting an observed behavior of a splicing system. The main idea is to input a marked DNA strand into a test tube together with certain restriction enzymes and, possibly, with other DNA strands. Under the action of the enzymes, the marked DNA strand starts to evolve by splicing with other DNA strands. The evolution of the marked DNA strand is “observed” by an outside observer and the input DNA strand is “accepted” if its (observed) evolution follows a certain expected pattern. We prove that using finite splicing system (finite set of rules and finite set of axioms), universal computation is attainable with simple observing and accepting devices made of finite state automata.

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Author information

Authors and Affiliations

  1. Department of Computer Science and Artificial Intelligence, University of Sevilla, Avda. Reina Mercedes s/n, 41012, Sevilla, Spain

    Matteo Cavaliere

  2. Department of Mathematics, University of South Florida, Tampa, FL, 33620, USA

    Nataša Jonoska

  3. Research Group on Mathematical Linguistics, Rovira i Virgili University, Pl. Imperial Tàrraco 1, 43005, Tarragona, Spain

    Peter Leupold

Authors
  1. Matteo Cavaliere
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  2. Nataša Jonoska
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  3. Peter Leupold
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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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© 2006 Springer-Verlag Berlin Heidelberg

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Cavaliere, M., Jonoska, N., Leupold, P. (2006). Recognizing DNA Splicing. 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_2

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  • DOI: https://doi.org/10.1007/11753681_2

  • 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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