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J Comput Biol. 2011 Mar;18(3):469-81. doi: 10.1089/cmb.2010.0252.

Cactus graphs for genome comparisons.

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1
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California, USA. benedict@soe.ucsc.edu

Abstract

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 www.liebertonline.com/cmb .

PMID:
21385048
DOI:
10.1089/cmb.2010.0252
[Indexed for MEDLINE]
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