Simple Operations for Gene Assembly (bibtex)
by Harju, Tero, Petre, Ion, Rogojin, Vladimir and Rozenberg, Grzegorz
Abstract:
The intramolecular model for gene assembly in ciliates considers three operations, $mld$, $mhi$, and $mdlad$ 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 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.
Reference:
Simple Operations for Gene Assembly (Harju, Tero, Petre, Ion, Rogojin, Vladimir and Rozenberg, Grzegorz), Technical report 757, , 2006.
Bibtex Entry:
@TechReport{t147,
  author   = {Harju, Tero AND Petre, Ion AND Rogojin, Vladimir AND Rozenberg, Grzegorz},
  title    = {Simple Operations for Gene Assembly},
  year     = {2006},
  number   = {757},
  abstract = {The intramolecular model for gene assembly in ciliates considers three operations, $mld$, $mhi$, and $mdlad$ 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 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.},
  keywords = {gene assembly, simple operations, signed permutations, sorting},
  pdf      = {pdfs/HPRG2006a.pdf},
}
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