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International Conference on Developments in Language Theory

DLT 2002: Developments in Language Theory pp 1–20Cite as

Computational Processes in Living Cells: Gene Assembly in Ciliates

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Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2450))

Abstract

One of the most complex DNA processing in nature known to us is carried out by ciliates during the sexual reproduction when their micronuclear genome is transformed to the macronuclear genome. This process of gene assembly is intriguing and captivating also from the computational point of view. We investigate here three intramolecular molecular operations (ld, hi, and dlad) postulated to accomplish gene assembly. The formal models for these operations are formulated on three different abstraction levels: MDS descriptors, legals strings and overlap graphs. In general both legal strings and overlap graphs contain strings and graphs that do not model any micronuclear gene. After a short survey of gene assembly we study the problem of recognizing whether a general legal string or a general overlap graph is a formalization of a micronuclear gene.

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Author information

Authors and Affiliations

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

    Tero Harju

  2. Leiden Institute for Advanced Computer Science, Leiden University, Niels Bohrweg 1, 2333, CA Leiden, the Netherlands

    Grzegorz Rozenberg

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

    Grzegorz Rozenberg

Authors
  1. Tero Harju
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  2. Grzegorz Rozenberg
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Editor information

Editors and Affiliations

  1. Faculty of Science and Faculty of Engineering, Kyoto Sangyo University, 603-8555, Kyoto, Japan

    Masami Ito  & Masafumi Toyama  & 

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© 2003 Springer-Verlag Berlin Heidelberg

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Harju, T., Rozenberg, G. (2003). Computational Processes in Living Cells: Gene Assembly in Ciliates. In: Ito, M., Toyama, M. (eds) Developments in Language Theory. DLT 2002. Lecture Notes in Computer Science, vol 2450. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45005-X_1

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  • DOI: https://doi.org/10.1007/3-540-45005-X_1

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-40431-6

  • Online ISBN: 978-3-540-45005-4

  • eBook Packages: Springer Book Archive

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