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Patterns of simple gene assembly in ciliates
Tekijät: Harju T, Petre I, Rogojin V, Rozenberg G
Kustantaja: ELSEVIER SCIENCE BV
Julkaisuvuosi: 2008
Lehti: Discrete Applied Mathematics
Tietokannassa oleva lehden nimi: DISCRETE APPLIED MATHEMATICS
Lehden akronyymi: DISCRETE APPL MATH
Vuosikerta: 156
Numero: 14
Aloitussivu: 2581
Lopetussivu: 2597
Sivujen määrä: 17
ISSN: 0166-218X
DOI: https://doi.org/10.1016/j.dam.2007.09.026
Tiivistelmä
The intramolecular model for gene assembly in ciliates considers three operations, Id, hi, and clad 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. (C) 2007 Elsevier B.V. All rights reserved.
The intramolecular model for gene assembly in ciliates considers three operations, Id, hi, and clad 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. (C) 2007 Elsevier B.V. All rights reserved.
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