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Simple Operations for Gene Assembly

Tero Harju, Ion Petre, Vladimir Rogojin, Grzegorz Rozenberg, Simple Operations for Gene Assembly. TUCS Technical Reports 757, Turku Centre for Computer Science, 2006.

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.

Files:

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BibTeX entry:

@TECHREPORT{tHaPeRoRo06a,
  title = {Simple Operations for Gene Assembly},
  author = {Harju, Tero and Petre, Ion and Rogojin, Vladimir and Rozenberg, Grzegorz},
  number = {757},
  series = {TUCS Technical Reports},
  publisher = {Turku Centre for Computer Science},
  year = {2006},
  keywords = {Gene assembly, simple operations, signed permutations, sorting},
  ISBN = {952-12-1701-4},
}

Belongs to TUCS Research Unit(s): Computational Biomodeling Laboratory (Combio Lab)

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