Inferring Orthology and Para
Inferring Orthology and Para
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DOI：
10.1007/978-1-61779-582-4_9
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发表时间：
2012-01-01
期刊：
影响因子：
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通讯作者：
Dessimoz, Christophe
中科院分区：
文献类型：
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作者：
Altenhoff, Adrian M.;Dessimoz, Christophe
同源基因和类似基因之间的区别，即通过物种形成和复制开始分化的基因，在广泛的背景下是相关的，最明显的是系统发育树推断和蛋白质功能注释。在本章中，我们概述了用来推断正形学和谬误学的方法。我们调查了基于图的方法（及其各种分组策略）和基于树的方法，它们解决了更普遍的基因/物种树调和问题。我们讨论了各种正字法推理方法和数据库之间的概念差异，并研究了验证和基准正字法预测的难题。最后，我们回顾了同源基因、类群和调和树的典型应用，并总结了对未来方法发展的思考。
The distinction between orthologs and paralogs, genes that started diverging by speciation versus duplication, is relevant in a wide range of contexts, most notably phylogenetic tree inference and protein function annotation. In this chapter, we provide an overview of the methods used to infer orthology and paralogy. We survey both graph-based approaches (and their various grouping strategies) and tree-based approaches, which solve the more general problem of gene/species tree reconciliation. We discuss conceptual differences among the various orthology inference methods and databases, and examine the difficult issue of verifying and benchmarking orthology predictions. Finally, we review typical applications of orthologous genes, groups, and reconciled trees and conclude with thoughts on future methodological developments.