A1 Vertaisarvioitu alkuperäisartikkeli tieteellisessä lehdessä
Simple operations for gene assembly
Tekijät: Harju T, Petre I, Rogojin V, Rozenberg G
Julkaisuvuosi: 2006
Lehti:: Lecture Notes in Computer Science
Tietokannassa oleva lehden nimi: DNA COMPUTING
Lehden akronyymi: LECT NOTES COMPUT SC
Vuosikerta: 3892
Aloitussivu: 96
Lopetussivu: 111
Sivujen määrä: 16
ISBN: 3-540-34161-7
ISSN: 0302-9743
Tiivistelmä
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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