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IMI/Publicaţii/CSJM/Ediţii/CSJM v.18, n.1 (52), 2010/

Three models for gene assembly in ciliates: a comparison

Authors: Miika Langille, Ion Petre, Rogojin Vladimir
Keywords: Ciliate, simple gene assembly, simple model, elementary model, confluence, completeness, characterization, sequential complexity, model validation, signed permutations, sorting.

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.

Miika Langille,
Department of IT, Abo Akademi University
ICT-building, Joukahaisenkatu 3-5 A, 5th floor
Turku 20520 Finland
E-mail:

Ion Petre,
Academy of Finland and
Turku Centre for Computer Science,
Department of Computer Science,
Abo Akademi University,
Turku 20520 Finland
E-mail:

Vladimir Rogojin,
Turku Centre for Computer Science,
Department of Computer Science,
Abo Akademi University,
Turku 20520 Finland
E-mail:

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