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Cactus Graphs for Genome Comparisons

  • Benedict Paten
  • Mark Diekhans
  • Dent Earl
  • John St. John
  • Jian Ma
  • Bernard Suh
  • David Haussler
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6044)

Abstract

We introduce a data structure, analysis and visualization scheme called a cactus graph for comparing sets of related genomes. Cactus graphs capture some of the advantages of de Bruijn and breakpoint graphs in one unified framework. They naturally decompose the common substructures in a set of related genomes into a hierarchy of chains that can be visualized as multiple alignments and nets that can be visualized in circular genome plots.

Keywords

Adjacency Edge Simple Cycle Adjacency Graph Origin Node Eulerian Circuit 
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 2010

Authors and Affiliations

  • Benedict Paten
    • 1
  • Mark Diekhans
    • 1
  • Dent Earl
    • 1
  • John St. John
    • 1
  • Jian Ma
    • 2
  • Bernard Suh
    • 1
  • David Haussler
    • 1
  1. 1.Center for Biomolecular Science and EngineeringUniversity of CaliforniaSanta CruzUSA
  2. 2.Department of BioengineeringUniversity of Illinois at Urbana-ChampaignUrbanaUSA

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