Cactus graphs for genome comparisons

Benedict Paten, Mark Diekhans, Dent Earl, John St John, Jian Ma, Bernard Suh, David Haussler

Research output: Contribution to journalArticlepeer-review


We introduce a data structure, analysis, and visualization scheme called a cactus graph for comparing sets of related genomes. In common with multi-break point graphs and A-Bruijn graphs, cactus graphs can represent duplications and general genomic rearrangements, but additionally, they naturally decompose the common substructures in a set of related genomes into a hierarchy of chains that can be visualized as two-dimensional multiple alignments and nets that can be visualized in circular genome plots. Supplementary Material is available at

Original languageEnglish (US)
Pages (from-to)469-481
Number of pages13
JournalJournal of Computational Biology
Issue number3
StatePublished - Mar 1 2011
Externally publishedYes


  • Algorithms
  • cancer genomics
  • genomic rearrangements
  • sequence analysis

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Modeling and Simulation
  • Computational Theory and Mathematics


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