Directed Overlap-Inclusion Graphs as Representations of Ciliate Genes

A1 Journal article (refereed)

Internal Authors/Editors

Publication Details

List of Authors: Sepinoud Azimi, Tero Harju, Miika Langille, Ion Petre, Vladimir Rogojin
Publisher: IOS Press
Publication year: 2011
Journal: Fundamenta Informaticae
Volume number: 110
Issue number: 1-4
Start page: 29
End page: 44
eISSN: 1875-8681


The simple intramolecular model for gene assembly in ciliates consists of three molecular operations based on local DNA manipulations. It was shown to predict correctly the assembly of all currently known ciliate gene patterns. 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. A different formalization in terms of overlap-inclusion graphs, recently introduced
by Brijder and Hoogeboom, proved well-suited to describe two of the three operations of the model and their combinatorial properties. We introduce in this paper an extension of the framework of Brijder and Hoogeboom in terms of directed overlap-inclusion graphs where more of the linear
structure of the ciliate genes is described. We investigate a number of combinatorial properties of
these graphs, including a necessary property in terms of forbidden induced subgraphs.

Last updated on 2020-15-08 at 04:42