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A Phylogenetic Approach to Genetic Map Refinement

  • Denis Bertrand
  • Mathieu Blanchette
  • Nadia El-Mabrouk
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5267)

Abstract

Following various genetic mapping techniques conducted on different segregating populations, one or more genetic maps are obtained for a given species. However, recombination analyses and other methods for gene mapping often fail to resolve the ordering of some pairs of neighboring markers, thereby leading to sets of markers ambiguously mapped to the same position. Each individual map is thus a partial order defined on the set of markers, and can be represented as a Directed Acyclic Graph (DAG). In this paper, given a phylogenetic tree with a set of DAGs labeling each leaf (species), the goal is to infer, at each leaf, a single combined DAG that is as resolved as possible, considering the complementary information provided by individual maps, and the phylogenetic information provided by the species tree. After combining the individual maps of a leaf into a single DAG, we order incomparable markers by using two successive heuristics for minimizing two distances on the species tree: the breakpoint distance, and the Kemeny distance. We apply our algorithms to the plant species represented in the Gramene database, and we evaluate the simplified maps we obtained.

Keywords

Directed Acyclic Graph Total Order Phylogenetic Information Phylogenetic Approach Strongly Connect Component 
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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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Denis Bertrand
    • 1
  • Mathieu Blanchette
    • 2
  • Nadia El-Mabrouk
    • 3
  1. 1.DIROUniversité de MontréalCanada
  2. 2.McGill Centre for BioinformaticsMcGill UniversityCanada
  3. 3.DIRO 

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