用于基因组比较的仙人掌图。
Cactus graphs for genome comparisons.
作者信息
Paten Benedict, Diekhans Mark, Earl Dent, John John St, Ma Jian, Suh Bernard, Haussler David
机构信息
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California, USA.
出版信息
J Comput Biol. 2011 Mar;18(3):469-81. doi: 10.1089/cmb.2010.0252.
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 .
摘要
我们引入了一种名为仙人掌图的数据结构、分析方法和可视化方案，用于比较相关基因组集合。与多断点图和A-布鲁因图一样，仙人掌图可以表示重复和一般的基因组重排，但此外，它们还能自然地将一组相关基因组中的共同子结构分解为链的层次结构，这些链可以可视化为二维多重比对，以及可以在环形基因组图中可视化的网络。补充材料可在www.liebertonline.com/cmb上获取。
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