Genomic scale sub-family assignment of protein domains.
Genomic scale sub-family assignment of protein domains.
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DOI：
10.1093/nar/gkl484
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发表时间：
2006
影响因子：
14.9
通讯作者：
Gough J
中科院分区：
文献类型：
--
作者：
Gough J
许多蛋白质和结构域的分类方案要么是分层的，要么是半分层的，但大多数数据库，尤其是那些提供全基因组分析的数据库，仅在其分层结构的某一级别提供序列分配。给定一个已建立的层次结构，将新序列分配给现有层次结构的较低级别的问题比需要检测最远关系的初始顶层分配要简单（但同样重要）。这里以新过程的形式描述了该问题的解决方案，该新过程可以被认为是成对方法和轮廓方法之间的混合。混合方法是一个通用过程，可以应用于任何预定义的层次结构、任何级别，原则上包括多个子级别。它已通过 SUPERFAMILY 数据库在 SCOP 分类上进行了测试，其性能明显优于单独的配对方法或剖面方法。与解决该问题的其他可能方法相比，混合方法的最大优点可能是在现有配置文件库的框架内，分配是完全自动的，并且几乎不需要额外的计算成本。因此，它已经在 SCOP 家族水平上应用于 SUPERFAMILY 数据库中的所有基因组，为生物和生物信息学界提供了大量的新数据。
Many classification schemes for proteins and domains are either hierarchical or semi-hierarchical yet most databases, especially those offering genome-wide analysis, only provide assignments to sequences at one level of their hierarchy. Given an established hierarchy, the problem of assigning new sequences to lower levels of that existing hierarchy is less hard (but no less important) than the initial top level assignment which requires the detection of the most distant relationships. A solution to this problem is described here in the form of a new procedure which can be thought of as a hybrid between pairwise and profile methods. The hybrid method is a general procedure that can be applied to any pre-defined hierarchy, at any level, including in principle multiple sub-levels. It has been tested on the SCOP classification via the SUPERFAMILY database and performs significantly better than either pairwise or profile methods alone. Perhaps the greatest advantage of the hybrid method over other possible approaches to the problem is that within the framework of an existing profile library, the assignments are fully automatic and come at almost no additional computational cost. Hence it has already been applied at the SCOP family level to all genomes in the SUPERFAMILY database, providing a wealth of new data to the biological and bioinformatics communities.
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