ProtoMap: automatic classification of protein sequences and hierarchy of protein families
ProtoMap: automatic classification of protein sequences and hierarchy of protein families
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DOI：
10.1093/nar/28.1.49
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发表时间：
2000-01-01
影响因子：
14.9
通讯作者：
Linial, M
中科院分区：
文献类型：
--
作者：
Yona, G;Linial, N;Linial, M
Protomap位点将瑞士蛋白数据库中所有蛋白质的详尽分类分为相关蛋白质组。该分类基于对蛋白质序列中所有成对相似性的分析，该分析使转移率的必不可少用于鉴定蛋白质之间的同源性。在分类的每个组中，每两个成员要么直接或传统相关。但是，为了防止无关蛋白质聚集在一起，限制性地应用了传递性，分类是在不同级别的置信度完成的，并产生了所有人的分层组织：蛋白质。所得的分类将蛋白质空间分为定义明确的蛋白质，这些蛋白质与天然生物家庭和超家族密切相关。许多簇包含其他数据库分类的蛋白质序列。我们的分析提出的分层组织可能有助于检测已知蛋白质家族中更细的亚家族。此外，它还带来了蛋白质家族之间有趣的关系，可以在其中勾勒出蛋白质家族附近的局部地图。可以通过http://www.protomap.cs.huji.ac.il访问Protomap Web服务器。
The ProtoMap site offers an exhaustive classification of all proteins in the SWISS-PROT database, into groups of related proteins. The classification is based on analysis of all pairwise similarities among protein sequences, The analysis makes essential use of transitivity to identify homologies among proteins. Within each group of the classification, every two members are either directly or transitively related. However, transitivity is applied restrictively in order to prevent unrelated proteins from clustering together, The classification is done at different levels of confidence, and yields a hierarchical organization of all:proteins. The resulting classification splits the protein space into well-defined groups of proteins, which are closely correlated with natural biological families and superfamilies. Many clusters contain protein sequences that are not classified by other databases. The hierarchical organization suggested by our analysis may help in detecting finer subfamilies in families of known proteins. In addition it brings forth interesting relationships between protein families, upon which local maps for the neighborhood of protein families can be sketched. The ProtoMap web server can be accessed at http://www.protomap.cs.huji.ac.il.