Correction of Weighted Orthology and Paralogy Relations - Complexity and Algorithmic Results

Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9838)

Abstract

A relation graph for a gene family is a graph with vertices representing the genes, edges connecting pairs of orthologous genes and “missing” edges representing paralogs. While a gene tree directly leads to a set of orthology and paralogy relations, the converse is not always true. Indeed a relation graph cannot necessarily be inferred from any tree, and even if it is “satisfiable” by a tree, this tree is not necessarily “consistent”, i.e. does not necessarily reflect a valid history for the genes, in agreement with a species tree. Here, we consider the problems of minimally correcting a relation graph for satisfiability and consistency, when a degree of confidence is assigned to each orthology or paralogy relation, leading to a weighted relation graph. We provide complexity and algorithmic results for minimizing corrections on a weighted graph, and also for the maximization variant of the problems for unweighted graphs.

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Riccardo Dondi
    • 1
  • Nadia El-Mabrouk
    • 2
  • Manuel Lafond
    • 2
  1. 1.Dipartimento di Lettere, Filosofia e ComunicazioneUniversità degli Studi di BergamoBergamoItaly
  2. 2.Department of Computer ScienceUniversité de MontréalMontréalCanada

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