Secator: a program for inferring protein subfamilies from phylogenetic trees.
Secator: a program for inferring protein subfamilies from phylogenetic trees.
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Secator：一个从系统发育树推断蛋白质亚家族的程序。
DOI：
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发表时间：
2001
影响因子：
10.7
通讯作者：
O. Poch
中科院分区：
文献类型：
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作者：
Nicolas Wicker;Guy;J. Thierry;O. Poch
随着蛋白质数据的大量增加，一个重要的问题是估计，在一个大的蛋白质家族，合理的子集的数量，为后续的深入结构，功能和进化分析。为了解决这个问题，我们开发了一个新程序Secator，它使用基于蛋白质序列多重比对的距离矩阵来实现升序分层方法的原理。通过引入一种新的终止规则，对系统树节点的相异度值进行划分，自动确定显著相异度值。通过单独的Jackknife研究验证了Secator获得的聚类质量。该方法被证明在24个大的蛋白质家族，涵盖了广泛的结构和序列的保守性和它的有用性和准确性与真实的生物数据上说明了两个研究充分的蛋白质家族（Sm蛋白和核受体）。
With the huge increase of protein data, an important problem is to estimate, within a large protein family, the number of sensible subsets for subsequent in-depth structural, functional, and evolutionary analyses. To tackle this problem, we developed a new program, Secator, which implements the principle of an ascending hierarchical method using a distance matrix based on a multiple alignment of protein sequences. Dissimilarity values assigned to the nodes of a deduced phylogenetic tree are partitioned by a new stopping rule introduced to automatically determine the significant dissimilarity values. The quality of the clusters obtained by Secator is verified by a separate Jackknife study. The method is demonstrated on 24 large protein families covering a wide spectrum of structural and sequence conservation and its usefulness and accuracy with real biological data is illustrated on two well-studied protein families (the Sm proteins and the nuclear receptors).