GraphML specializations to codify ancestral recombinant graphs.
GraphML specializations to codify ancestral recombinant graphs.
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DOI：
10.3389/fgene.2013.00146
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发表时间：
2013
影响因子：
3.7
通讯作者：
Kuhner MK
中科院分区：
文献类型：
--
作者：
McGill JR;Walkup EA;Kuhner MK
模拟、推断或分析祖先重组图（arg）的软件面临着如何传达它们的问题。现有的格式要么忽略了染色体上重组的位置信息，要么忽略了重组相对于分支拓扑结构的位置信息。我们提出了GraphML的专门化，这是一个基于xml的数学图标准，用于arg的通信。GraphML <node>类型专门用于包含节点类型、时间、重组位置和名称。GraphML <edge>类型专门用于包含沿该边传递的祖先材料。这种方法（我们称之为ArgML）保留了原始ARG中的所有信息。由于使用了已建立的格式，ArgML可以被现有的软件解析、检查和显示。
Software which simulates, infers, or analyzes ancestral recombination graphs (ARGs) faces the problem of communicating them. Existing formats omit information either about the location of recombinations along the chromosome or the position of recombinations relative to the branching topology. We present a specialization of GraphML, an XML-based standard for mathematical graphs, for communication of ARGs. The GraphML <node> type is specialized to contain the node type, time, recombination location, and name. The GraphML <edge> type is specialized to contain the ancestral material passed along that edge. This approach, which we call ArgML, retains all information in the original ARG. Due to its use of established formats ArgML can be parsed, checked and displayed by existing software.