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Efficient Bubble Enumeration in Directed Graphs

  • Etienne Birmelé
  • Pierluigi Crescenzi
  • Rui Ferreira
  • Roberto Grossi
  • Vincent Lacroix
  • Andrea Marino
  • Nadia Pisanti
  • Gustavo Sacomoto
  • Marie-France Sagot
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7608)

Abstract

Polymorphisms in DNA- or RNA-seq data lead to recognisable patterns in a de Bruijn graph representation of the reads obtained by sequencing. Such patterns have been called mouths, or bubbles in the literature. They correspond to two vertex-disjoint directed paths between a source s and a target t. Due to the high number of such bubbles that may be present in real data, their enumeration is a major issue concerning the efficiency of dedicated algorithms. We propose in this paper the first linear delay algorithm to enumerate all bubbles with a given source.

Keywords

Directed Graph Alternative Splice Event Next Generation Sequencing Data Linear Delay Target Vertex 
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

  • Etienne Birmelé
    • 1
    • 3
  • Pierluigi Crescenzi
    • 4
  • Rui Ferreira
    • 5
  • Roberto Grossi
    • 5
  • Vincent Lacroix
    • 1
    • 2
  • Andrea Marino
    • 1
    • 4
  • Nadia Pisanti
    • 5
  • Gustavo Sacomoto
    • 1
    • 2
  • Marie-France Sagot
    • 1
    • 2
  1. 1.INRIA Grenoble Rhône-AlpesFrance
  2. 2.Université de Lyon 1VilleurbanneFrance
  3. 3.Université d’ÉvryFrance
  4. 4.Dipartimento di Sistemi e InformaticaUniversità di FirenzeFirenzeItaly
  5. 5.Dipartimento di InformaticaUniversità di PisaPisaItaly

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