Applicability of Loop Recombination in Ciliates Using the Breakpoint Graph

  • Robert Brijder
  • Hendrik Jan Hoogeboom
  • Michael Muskulus
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4216)

Abstract

The concept of breakpoint graph, known from the theory of sorting by reversal, has been successfully applied in the theory of gene assembly in ciliates. We further investigate its usage for gene assembly, and show that the graph allows for an efficient characterization of the possible orders of loop recombination operations (one of the three types of molecular operations that accomplish gene assembly) for a given gene during gene assembly. The characterization is based on spanning trees within a graph built upon the connected components in the breakpoint graph. We work in the abstract and more general setting of so-called legal strings.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Robert Brijder
    • 1
  • Hendrik Jan Hoogeboom
    • 1
  • Michael Muskulus
    • 2
  1. 1.Leiden Institute of Advanced Computer ScienceUniversiteit LeidenLeidenThe Netherlands
  2. 2.Mathematical InstituteUniversiteit LeidenLeidenThe Netherlands

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