Cactus graphs for genome comparisons

Authors:
Benedict Paten;Mark Diekhans;Dent Earl;John St John;Jian Ma;Bernard Suh;David Haussler
Affiliations:
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA;Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA;Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA;Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA;Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL;Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA;Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA
Venue:
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
Year:
2010

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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.