MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score.
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score.
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DOI：
10.1093/nar/gkq953
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发表时间：
2011-03
影响因子：
14.9
通讯作者：
Gabaldón T
中科院分区：
文献类型：
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作者：
Pryszcz LP;Huerta-Cepas J;Gabaldón T
可靠的矫正预测是比较基因组学的核心。基于系统发育分析的方法非常类似于矫形和副本的原始定义，并且已知高度准确。但是，与这些分析相关的大量计算成本是一个限制因素，通常阻止其在基因组尺度上使用。最近，一些项目解决了可以推断出正交和旁拉关系的大量高质量系统发育树的重建。这为我们提供了从多个独立的系统发育树中推断基因的进化关系的机会。使用这种策略，我们结合了从不同数据库中得出的系统发育信息，以预测829个完全测序基因组中410万个蛋白质的矫正和招聘关系。我们表明，进行预测的独立来源的数量以及预测之间的一致性水平可以用作可靠的置信度得分。已经开发了一个Web服务器，可以轻松访问这些数据（http://orthology.phylomedb.org），该数据为用户提供了基于系统发育的矫形器和催化性预测的全球存储库。
Reliable prediction of orthology is central to comparative genomics. Approaches based on phylogenetic analyses closely resemble the original definition of orthology and paralogy and are known to be highly accurate. However, the large computational cost associated to these analyses is a limiting factor that often prevents its use at genomic scales. Recently, several projects have addressed the reconstruction of large collections of high-quality phylogenetic trees from which orthology and paralogy relationships can be inferred. This provides us with the opportunity to infer the evolutionary relationships of genes from multiple, independent, phylogenetic trees. Using such strategy, we combine phylogenetic information derived from different databases, to predict orthology and paralogy relationships for 4.1 million proteins in 829 fully sequenced genomes. We show that the number of independent sources from which a prediction is made, as well as the level of consistency across predictions, can be used as reliable confidence scores. A webserver has been developed to easily access these data (http://orthology.phylomedb.org), which provides users with a global repository of phylogeny-based orthology and paralogy predictions.
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影响因子：
4.3
作者：
Altenhoff, Adrian M.;Dessimoz, Christophe
通讯作者：
Dessimoz, Christophe
影响因子：
12.3
作者：
Gabaldón T
通讯作者：
Gabaldón T
影响因子：
7
作者：
Vilella, Albert J.;Severin, Jessica;Birney, Ewan
通讯作者：
Birney, Ewan
影响因子：
14.9
作者：
Datta RS;Meacham C;Samad B;Neyer C;Sjölander K
通讯作者：
Sjölander K
人类的前线。
影响因子：
12.3
作者：
通讯作者：
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