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Inferring Positional Homologs with Common Intervals of Sequences

  • Guillaume Blin
  • Annie Chateau
  • Cedric Chauve
  • Yannick Gingras
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4205)

Abstract

Inferring orthologous and paralogous genes is an important problem in whole genomes comparisons, both for functional or evolutionary studies. In this paper, we introduce a new approach for inferring candidate pairs of orthologous genes between genomes, also called positional homologs, based on the conservation of the genomic context. We consider genomes represented by their gene order – i.e. sequences of signed integers – and common intervals of these sequences as the anchors of the final gene matching. We show that the natural combinatorial problem of computing a maximal cover of the two genomes using the minimum number of common intervals is NP-complete and we give a simple heuristic for this problem. We illustrate the effectiveness of this first approach using common intervals of sequences on two datasets, respectively 8 γ-proteobacterial genomes and the human and mouse whole genomes.

Keywords

Gene Pair Orthologous Gene Maximal Subset Common Interval Xylella Fastidiosa 
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 2006

Authors and Affiliations

  • Guillaume Blin
    • 1
  • Annie Chateau
    • 2
    • 3
  • Cedric Chauve
    • 2
    • 3
    • 4
  • Yannick Gingras
    • 3
  1. 1.IGM-LabInfo – UMR CNRS 8049Université Marne-la-ValléeMarne-la-ValléeFrance
  2. 2.LaCIMUniversité du Québec À MontréalMontréalCanada
  3. 3.CGLUniversité du Québec ÀMontréal
  4. 4.Department of MathematicsSimon Fraser UniversityBurnabyCanada

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