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Inferring Positional Homologs with Common Intervals of Sequences

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Comparative Genomics (RCG 2006)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4205))

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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.

Work supported by grants from Génome Québec, NSERC and Coopération Franco-Québecoise.

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Author information

Authors and Affiliations

  1. IGM-LabInfo – UMR CNRS 8049, Université Marne-la-Vallée, 5 bd. Descartes, 77454 Cedex 2, Marne-la-Vallée, France

    Guillaume Blin

  2. LaCIM, Université du Québec À Montréal, CP 8888, Succ. Centre-Ville, H3C 3P8, Montréal, (QC), Canada

    Annie Chateau & Cedric Chauve

  3. CGL, Université du Québec À, Montréal

    Annie Chateau, Cedric Chauve & Yannick Gingras

  4. Department of Mathematics, Simon Fraser University, 8888 University Drive, V5A 1S6, Burnaby, (BC), Canada

    Cedric Chauve

Authors
  1. Guillaume Blin
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  2. Annie Chateau
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  3. Cedric Chauve
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  4. Yannick Gingras
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Editor information

Editors and Affiliations

  1. Genome Institute of Singapore, 138672, Republic of Singapore

    Guillaume Bourque

  2. DIRO, Université de Montréal, H3C 3J7, Canada

    Nadia El-Mabrouk

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© 2006 Springer-Verlag Berlin Heidelberg

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Blin, G., Chateau, A., Chauve, C., Gingras, Y. (2006). Inferring Positional Homologs with Common Intervals of Sequences. In: Bourque, G., El-Mabrouk, N. (eds) Comparative Genomics. RCG 2006. Lecture Notes in Computer Science(), vol 4205. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11864127_3

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  • DOI: https://doi.org/10.1007/11864127_3

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-44529-6

  • Online ISBN: 978-3-540-44530-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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