Three models for gene assembly in ciliates: a comparison

Authors:
Miika Langille;Ion Petre;Vladimir Rogojin
Affiliations:
Åbo Akademi University, Joukahaisenkatu, Finland;Åbo Akademi University, Joukahaisenkatu, Finland;Åbo Akademi University, Joukahaisenkatu, Finland
Venue:
Proceedings of the 3rd International Conference on Bio-Inspired Models of Network, Information and Computing Sytems
Year:
2008

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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.