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The Reduction Power of Simple Operations for Gene Assembly in Ciliates

Sepinoud Azimi, Ion Petre, The Reduction Power of Simple Operations for Gene Assembly in Ciliates. In: Gheorghe Paun, Grzegorz Rozenberg, Arto Salomaa (Eds.), Discrete Mathematics and Computer Science, 23–36, The Publishing House of the Romanian Academy, 2014.

Abstract:

The simple intramolecular model for gene assembly in ciliates predicts correctly the assembly of all currently known ciliate gene patterns. The model consists of three molecular operations: the ld (loop,
direct-repeat excision), the simple hi (hairpin, inverted-repeat recombination), and the simple dlad (double-loop alternating direct-repeat recombination)
operations. The gene transformations conjectured by the simple intramolecular model for gene assembly can be studied as operations on the so-called directed-overlap inclusion (in short, DOI) graphs. In this paper we focus on characterizing the DOI graphs that are reducible using only some combinations of the three simple operations. We also show that the DOI graph model is confluent.

BibTeX entry:

@INBOOK{jAzPe14a,
  title = {The Reduction Power of Simple Operations for Gene Assembly in Ciliates},
  booktitle = {Discrete Mathematics and Computer Science},
  author = {Azimi, Sepinoud and Petre, Ion},
  editor = {Paun, Gheorghe and Rozenberg, Grzegorz and Salomaa, Arto},
  publisher = {The Publishing House of the Romanian Academy},
  pages = {23–36},
  year = {2014},
  keywords = {Directed overlap-inclusion graphs, gene assembly in ciliates, simple operations, confluent},
}

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

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