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Parallelism in Gene Assembly

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“One of the oldest forms of life on Earth has been revealed as a natural born computer programmer.”

Abstract

The process of gene assembly in ciliates, an ancient group of organisms, is one of the most complex instances of DNA manipulation known in any organisms. This process is fascinating from the computational point of view, with ciliates even using the linked lists data structure. Three molecular operations (ld, hi, and dlad) have been postulated for the gene assembly process. We initiate here the study of parallelism in this process, raising several natural questions, such as: when can a number of operations be applied in parallel to a gene pattern; or how many steps are needed to assemble (in parallel) a micronuclear gene. In particular, this gives rise to a new measure of complexity for the process of gene assembly in ciliates.

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Authors and Affiliations

  1. Department of Mathematics, University of Turku, Turku Center for Computer Science, FIN-20014, Turku, Finland

    Tero Harju

  2. Department of Computer Science, Åbo Akademi University, Turku Center for Computer Science, FIN-20520, Turku, Finland

    Chang Li

  3. Academy of Finland and Department of Computer Science, Åbo Akademi University, Turku Center for Computer Science, FIN-20520, Turku, Finland

    Ion Petre

  4. Leiden Institute for Advanced Computer Science, Leiden University, 2333, CA, Leiden, The Netherlands

    Grzegorz Rozenberg

  5. Department of Computer Science, University of Colorado, Boulder, CO, 80309-0347, USA

    Grzegorz Rozenberg

Authors
  1. Tero Harju
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  2. Chang Li
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  3. Ion Petre
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  4. Grzegorz Rozenberg
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Corresponding author

Correspondence to Grzegorz Rozenberg.

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Harju, T., Li, C., Petre, I. et al. Parallelism in Gene Assembly. Nat Comput 5, 203–223 (2006). https://doi.org/10.1007/s11047-005-4462-0

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  • DOI: https://doi.org/10.1007/s11047-005-4462-0

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