3d International ICST Conference on Bio-Inspired Models of Network, Information, and Computing Systems

Research Article

Three models for gene assembly in ciliates: a comparison

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  • @INPROCEEDINGS{10.4108/ICST.BIONETICS2008.4689,
        author={Miika Langille and Ion Petre and Vladimir Rogojin},
        title={Three models for gene assembly in ciliates: a comparison},
        proceedings={3d International ICST Conference on Bio-Inspired Models of Network, Information, and Computing Systems},
        publisher={ICST},
        proceedings_a={BIONETICS},
        year={2010},
        month={5},
        keywords={ciliate simple gene assembly simple model elementary model confluence completeness characterization sequential complexity model validation signed permutations sorting},
        doi={10.4108/ICST.BIONETICS2008.4689}
    }
    
  • Miika Langille
    Ion Petre
    Vladimir Rogojin
    Year: 2010
    Three models for gene assembly in ciliates: a comparison
    BIONETICS
    ICST
    DOI: 10.4108/ICST.BIONETICS2008.4689
Miika Langille1,*, Ion Petre2,*, Vladimir Rogojin3,*
  • 1: Department of IT, Åbo Akademi University, ICT-building, Joukahaisenkatu 3-5 A, 5th floor Turku 20520 Finland
  • 2: Academy of Finland, and Turku Centre for Computer Science Department of IT, Åbo Akademi University, ICT-building, Joukahaisenkatu 3-5 A, 5th floor Turku 20520 Finland
  • 3: Turku Centre for Computer Science Department of IT, Åbo Akademi University ICT-building, Joukahaisenkatu 3-5 A, 5th floor Turku 20520 Finland
*Contact email: miika.langille@abo.fi, ion.petre@abo.fi, vladimir.rogojin@abo.fi

Abstract

We survey in this paper the main differences among three variants of an intramolecular model for gene assembly: the general, the simple, and the elementary models. We present all of them in terms of sorting signed permutations and compare their behavior with respect to: (i) completeness, (ii) confluence (with the notion defined in three different setups), (iii) decidability, (iv) characterization of the sortable permutations in each model, (v) sequential complexity, and (vi) experimental validation.