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Simple Gene Assembly as a Rewriting of Directed Overlap-Inclusion Graphs

Sepinoud Azimi, Tero Harju, Miika Langille, Ion Petre, Simple Gene Assembly as a Rewriting of Directed Overlap-Inclusion Graphs. TUCS Technical Reports 1030, Turku Centre for Computer Science, 2011.

Abstract:

The simple intramolecular model for gene assembly in ciliates consists of three molecular operations, simple ld, simple hi and simple dlad. Mathematical models in terms of signed permutations and signed strings proved limited in capturing some of the combinatorial details of the simple gene assembly process. Brijder and Hoogeboom introduced a new model in terms of overlap-inclusion graphs which could describe two of the three operations of the model and their combinatorial properties. To capture the third operation, we extended their framework to directed overlap-inclusion (DOI) graphs. In this paper we introduce DOI graph-based rewriting rules that capture all three operations of the simple gene assembly model and prove that they are equivalent to the string-based formalization of the model.

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BibTeX entry:

@TECHREPORT{tAzLaPe11a,
  title = {Simple Gene Assembly as a Rewriting of Directed Overlap-Inclusion Graphs},
  author = {Azimi, Sepinoud and Harju, Tero and Langille, Miika and Petre, Ion},
  number = {1030},
  series = {TUCS Technical Reports},
  publisher = {Turku Centre for Computer Science},
  year = {2011},
  keywords = {Simple gene assembly, Directed overlap inclusion graphs, Graph-based simple operations},
  ISBN = {978-952-12-2688-5},
}

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

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