Patterns of simple gene assembly in ciliates |
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Authors: | Tero Harju Ion Petre Vladimir Rogojin Grzegorz Rozenberg |
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Institution: | aDepartment of Mathematics, University of Turku, Turku 20014, Finland;bAcademy of Finland and Department of Information Technologies, Åbo Akademi University, Turku 20520, Finland;cTurku Centre for Computer Science, Department of Information Technologies, Åbo Akademi University, Turku 20520, Finland;dLeiden Institute for Advanced Computer Science, Niels Bohrweg 1, 2333 CA Leiden, The Netherlands |
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Abstract: | The intramolecular model for gene assembly in ciliates considers three operations, , , and that can assemble any gene pattern through folding and recombination: the molecule is folded so that two occurrences of a pointer (short nucleotide sequence) get aligned and then the sequence is rearranged through recombination of pointers. In general, the sequence rearranged by one operation can be arbitrarily long and consist of many coding and noncoding blocks. We consider in this paper simple variants of the three operations, where only one coding block is rearranged at a time. We characterize in this paper the gene patterns that can be assembled through these variants. Our characterization is in terms of signed permutations and dependency graphs. Interestingly, we show that simple assemblies possess rather involved properties: a gene pattern may have both successful and unsuccessful assemblies and also more than one successful assembling strategy. |
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Keywords: | Gene assembly Simple operations Signed permutations Sorting |
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