An Algorithmic View on Multi-Related-Segments: A Unifying Model for Approximate Common Interval

  • Xiao Yang
  • Florian Sikora
  • Guillaume Blin
  • Sylvie Hamel
  • Romeo Rizzi
  • Srinivas Aluru
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7287)

Abstract

A set of genes that are proximately located on multiple chromosomes often implies their origin from the same ancestral genomic segment or their involvement in the same biological process. Among the numerous studies devoted to model and infer these gene sets, the recently introduced approximate common interval (ACI) models capture gene loss events in addition to the gene insertion, duplication and inversion events already incorporated by earlier models. However, the computational tractability of the corresponding problems remains open in most of the cases. In this contribution, we propose an algorithmic study of a unifying model for ACI, namely Multi-related-segments, and demonstrate that capturing gene losses induces intractability in many cases.

Keywords

Gene Loss Ancestral Gene Inversion Event Input String Gene Insertion 
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 2012

Authors and Affiliations

  • Xiao Yang
    • 1
  • Florian Sikora
    • 2
    • 5
  • Guillaume Blin
    • 2
  • Sylvie Hamel
    • 3
  • Romeo Rizzi
    • 4
  • Srinivas Aluru
    • 6
  1. 1.GSAPBroad Institute of MIT & HarvardUSA
  2. 2.LIGM, UMR 8049Université Paris-EstFrance
  3. 3.DIROUniversité de MontréalCanada
  4. 4.DIMIUniversità di UdineUdineItaly
  5. 5.Lehrstuhl für BioinformatikFriedrich-Schiller-Universität JenaGermany
  6. 6.DECEIowa State UniversityUSA

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