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Maximizing Synteny Blocks to Identify Ancestral Homologs

  • Guillaume Bourque
  • Yasmine Yacef
  • Nadia El-Mabrouk
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3678)

Abstract

Most genome rearrangement studies are based on the assumption that the compared genomes contain unique gene copies. This is clearly unsuitable for species with duplicated genes or when local alignment tools provide many ambiguous hits for the same gene. In this paper, we compare different measures of order conservation to select, among a gene family, the pair of copies in two genomes that best reflects the common ancestor. Specifically, we present algorithms to identify ancestral homologs, or exemplars [1] , by maximizing synteny blocks between genomes. Using simulated data, we validate our approach and show the merits of using a conservative approach when making such assignments.

Keywords

Genome Rearrangement Conjunctive Normal Form Synteny Block False Prediction Breakpoint Distance 
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 2005

Authors and Affiliations

  • Guillaume Bourque
    • 1
  • Yasmine Yacef
    • 2
  • Nadia El-Mabrouk
    • 2
  1. 1.Genome Institute of SingaporeSingapore
  2. 2.DIROUniversité de MontréalCanada

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