Annual International Conference on Research in Computational Molecular Biology

RECOMB 2010: Research in Computational Molecular Biology pp 410-425

Cactus Graphs for Genome Comparisons

  • Benedict Paten
  • Mark Diekhans
  • Dent Earl
  • John St. John
  • Jian Ma
  • Bernard Suh
  • David Haussler
Conference paper

DOI: 10.1007/978-3-642-12683-3_27

Volume 6044 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Paten B. et al. (2010) Cactus Graphs for Genome Comparisons. In: Berger B. (eds) Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044. Springer, Berlin, Heidelberg

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.

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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