Cactus Graphs for Genome Comparisons | Zendy

Benedict Paten | Zendy; Mark Diekhans | Zendy; Dent Earl | Zendy; John St. John | Zendy; Jian Ma | Zendy; Bernard Suh | Zendy; David Haussler | Zendy

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Cactus Graphs for Genome Comparisons

Author(s) -

Benedict Paten,

Mark Diekhans,

Dent Earl,

John St. John,

Jian Ma,

Bernard Suh,

David Haussler

Publication year - 2011

Publication title -

journal of computational biology

Language(s) - English

Resource type - Book series

SCImago Journal Rank - 0.585

H-Index - 95

eISSN - 1557-8666

pISSN - 1066-5277

ISBN - 3-642-12682-0

DOI - 10.1089/cmb.2010.0252

Subject(s) - genome , cactus , de bruijn graph , computer science , set (abstract data type) , theoretical computer science , visualization , de bruijn sequence , biology , data structure , graph , combinatorics , mathematics , data mining , genetics , gene , botany , programming language

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 .

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