A1 Refereed original research article in a scientific journal
Patterns of simple gene assembly in ciliates
Authors: Harju T, Petre I, Rogojin V, Rozenberg G
Publisher: ELSEVIER SCIENCE BV
Publication year: 2008
Journal:: Discrete Applied Mathematics
Journal name in source: DISCRETE APPLIED MATHEMATICS
Journal acronym: DISCRETE APPL MATH
Volume: 156
Issue: 14
First page : 2581
Last page: 2597
Number of pages: 17
ISSN: 0166-218X
DOI: https://doi.org/10.1016/j.dam.2007.09.026
Abstract
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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