Weighted genome trees: Refinements and applications
Weighted genome trees: Refinements and applications
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DOI：
10.1128/jb.187.4.1305-1316.2005
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发表时间：
2005-02-01
影响因子：
3.2
通讯作者：
Charlebois, RL
中科院分区：
文献类型：
--
作者：
Gophna, U;Doolittle, WF;Charlebois, RL
有许多方法可以将完整的基因组序列分组为反映其基因之间关系的分层模式（树）。这样的分组帮助我们组织生物信息，并对基因组和有机体进化的基本过程至关重要。基因组树利用了所有可比较的基因，但可以根据基因组之间的相似性、一致的相似性模式或普遍性来对这些基因的贡献进行不同的加权。在这里，我们探讨这种可能的加权策略，在142个原核和5个真核基因组的分析。我们表明，交替加权策略有不同的优势，我们提出，每个可能有其特定的用途，在系统或进化生物学。比较不同方法得到的结果可以为基因组进化中的重大事件和过程提供进一步的线索。
There are many ways to group completed genome sequences in hierarchical patterns (trees) reflecting relationships between their genes. Such groupings help us organize biological information and bear crucially on underlying processes of genome and organismal evolution. Genome trees make use of all comparable genes but can variously weight the contributions of these genes according to similarity, congruent patterns of similarity, or prevalence among genomes. Here we explore such possible weighting strategies, in an analysis of 142 prokaryotic and 5 eukaryotic genomes. We demonstrate that alternate weighting strategies have different advantages, and we propose that each may have its specific uses in systematic or evolutionary biology. Comparisons of results obtained with different methods can provide further clues to major events and processes in genome evolution.