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Overlap Graphs

  • Andrzej Ehrenfeucht
  • Tero Harju
  • Ion Petre
  • David M. Prescott
  • Grzegorz Rozenberg
Part of the Natural Computing Series book series (NCS)

Abstract

All formalizations of MDS structure of micronuclear or intermediate genes that we have considered until now (viz., micronuclear arrangements, MDS descriptors, and legal strings) were done in the framework of strings. We will move now to a different mathematical framework by formalizing MDS structure of genes as graphs. This transition from strings to graphs is obtained by considering the overlap graphs of legal strings. Each pointer set occurring in a legal string determines the substring of this string delimited by the two occurrences of this pointer set, and the overlap graph of a legal string represents the overlapping structures of all such substrings. In this chapter we introduce the basic notions concerning overlap graphs and study their relationship to (realistic) legal strings.

Keywords

Simple Graph Hamiltonian Path Signed Graph Circle Graph Chord Diagram 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Notes on References

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    Harju, T., Petre, I., and Rozenberg, G., Formal properties of gene assembly: Equivalence problem for overlap graphs. To appear.Google Scholar
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    Harju, T., and Rozenberg, G., Computational processes in living cells: gene assembly in ciliates. Lecure Notes in Comput. Sci. 2450 (2003) 1–20MathSciNetCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Andrzej Ehrenfeucht
    • 1
  • Tero Harju
    • 2
  • Ion Petre
    • 3
  • David M. Prescott
    • 4
  • Grzegorz Rozenberg
    • 5
  1. 1.Department of Computer ScienceUniversity of ColoradoBoulderUSA
  2. 2.Department of MathematicsUniversity of TurkuTurkuFinland
  3. 3.Department of Computer ScienceÅbo Akademi UniversityTurkuFinland
  4. 4.Department of Molecular, Cellular and Developmental BiologyUniversity of ColoradoBoulderUSA
  5. 5.Leiden Institute for Advanced Computer ScienceLeiden UniversityLeidenThe Netherlands

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