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The Algorithmic of Gene Teams

  • Anne Bergeron
  • Sylvie Corteel
  • Mathieu Raffinot
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2452)

Abstract

Comparative genomics is a growing field in computational biology, and one of its typical problem is the identification of sets of orthologous genes that have virtually the same function in several genomes. Many different bioinformatics approaches have been proposed to define these groups, often based on the detection of sets of genes that are “not too far” in all genomes. In this paper, we propose a unifying concept, called gene teams, which can be adapted to various notions of distance. We present two algorithms for identifying gene teams formed by n genes placed on m linear chromosomes. The first one runs in O(m 2 n 2) time, and follows a direct and simple approach. The second one is more tricky, but its running time is O(mnlog2(n)). Both algorithms require linear space. We also discuss extensions to circular chromosomes that achieve the same complexity.

Keywords

Time Complexity Polynomial Algorithm Recursive Call Nucleic Acid Research Circular Chromosome 
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 2002

Authors and Affiliations

  • Anne Bergeron
    • 1
    • 2
  • Sylvie Corteel
    • 3
  • Mathieu Raffinot
    • 4
  1. 1.LaCIMUniversité du Québec à MontréalCanada
  2. 2.Institut Gaspard-MongeUniversité Marne-la-ValléeFrance
  3. 3.CNRS - Laboratoire PRiSMUniversité de VersaillesVersailles cedexFrance
  4. 4.CNRS - Laboratoire Génome et InformatiqueEvryFrance

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