Three models for gene assembly in ciliates: a comparison

Miika Langille; Ion Petre; Vladimir Rogojin

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.

Keywords: ciliate simple gene assembly simple model elementary model confluence completeness characterization sequential complexity model validation signed permutations sorting

Published: 2010-05-16
Publisher: ICST
Modified: 2010-05-16

: http://dx.doi.org/10.4108/ICST.BIONETICS2008.4689

Three models for gene assembly in ciliates: a comparison

Abstract

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