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Simple Operations for Gene Assembly

Tero Harju, Ion Petre, Vladimir Rogojin, Grzegorz Rozenberg, Simple Operations for Gene Assembly. In: Alessandra Carbone, Niles A. Pierce (Eds.), Proceedings of 11th International Meeting on DNA Computing, DNA11, Lecture Notes in Computer Science, 96–111, Springer, 2005.

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 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 assembly.

BibTeX entry:

@INPROCEEDINGS{inpHaPeRoRo05a,
  title = {Simple Operations for Gene Assembly},
  booktitle = {Proceedings of 11th International Meeting on DNA Computing, DNA11},
  author = {Harju, Tero and Petre, Ion and Rogojin, Vladimir and Rozenberg, Grzegorz},
  series = {Lecture Notes in Computer Science},
  editor = {Carbone, Alessandra and Pierce, Niles A.},
  publisher = {Springer},
  pages = {96–111},
  year = {2005},
}

Belongs to TUCS Research Unit(s): FUNDIM, Fundamentals of Computing and Discrete Mathematics, Computational Biomodeling Laboratory (Combio Lab)

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