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Simple Operations for Gene Assembly

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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

The intramolecular model for gene assembly in ciliates considers three operations, ld, hi, and dlad that can assemble any gene pattern through folding and recombination: the molecule is folded so that two occurrences of a pointer (short nucleotide sequence) get aligned and then the sequence is rearranged through recombination of pointers. In general, the sequence rearranged by one operation can be arbitrarily long and consist of many coding and non-coding blocks. We consider in this paper some simpler variants of the three operations, where only one coding block is rearranged at a time. We characterize in this paper the gene patterns that can be assembled through these variants. Our characterization is in terms of signed permutations and dependency graphs. Interestingly, we show that simple assemblies possess rather involved properties: a gene pattern may have both successful and unsuccessful assemblies and also more than one successful assembling strategy.

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Author information

Authors and Affiliations

  1. Department of Mathematics, University of Turku, Turku, 20014, Finland

    Tero Harju

  2. Academy of Finland, Finland

    Ion Petre

  3. Department of Computer Science, Åbo Akademi University, Turku, 20520, Finland

    Ion Petre & Vladimir Rogojin

  4. Turku Centre for Computer Science, Turku, 20520, Finland

    Tero Harju, Ion Petre & Vladimir Rogojin

  5. Leiden Institute for Advanced Computer Science, Leiden University, Niels Bohrweg 1, 2333 CA, Leiden, The Netherlands

    Grzegorz Rozenberg

  6. Department of Computer Science, University of Colorado at Boulder, Boulder, Co, 80309-0347, USA

    Grzegorz Rozenberg

Authors
  1. Tero Harju
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  2. Ion Petre
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  3. Vladimir Rogojin
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  4. Grzegorz Rozenberg
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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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Harju, T., Petre, I., Rogojin, V., Rozenberg, G. (2006). Simple Operations for Gene Assembly. 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_8

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  • DOI: https://doi.org/10.1007/11753681_8

  • 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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