A1 Refereed original research article in a scientific journal
Simple operations for gene assembly
Authors: Harju T, Petre I, Rogojin V, Rozenberg G
Publication year: 2006
Journal:: Lecture Notes in Computer Science
Journal name in source: DNA COMPUTING
Journal acronym: LECT NOTES COMPUT SC
Volume: 3892
First page : 96
Last page: 111
Number of pages: 16
ISBN: 3-540-34161-7
ISSN: 0302-9743
Abstract
The intramolecular model for gene assembly in ciliates considers three operations, Id, hi, and dlad 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 non-coding blocks. We consider in this paper some simpler 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.
The intramolecular model for gene assembly in ciliates considers three operations, Id, hi, and dlad 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 non-coding blocks. We consider in this paper some simpler 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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