Emanuelsson Olof, Brunak Søren, von Heijne Gunnar, Nielsen Henrik
Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-10691 Stockholm, Sweden.
Nat Protoc. 2007;2(4):953-71. doi: 10.1038/nprot.2007.131.
Determining the subcellular localization of a protein is an important first step toward understanding its function. Here, we describe the properties of three well-known N-terminal sequence motifs directing proteins to the secretory pathway, mitochondria and chloroplasts, and sketch a brief history of methods to predict subcellular localization based on these sorting signals and other sequence properties. We then outline how to use a number of internet-accessible tools to arrive at a reliable subcellular localization prediction for eukaryotic and prokaryotic proteins. In particular, we provide detailed step-by-step instructions for the coupled use of the amino-acid sequence-based predictors TargetP, SignalP, ChloroP and TMHMM, which are all hosted at the Center for Biological Sequence Analysis, Technical University of Denmark. In addition, we describe and provide web references to other useful subcellular localization predictors. Finally, we discuss predictive performance measures in general and the performance of TargetP and SignalP in particular.
确定蛋白质的亚细胞定位是了解其功能的重要第一步。在这里，我们描述了三种将蛋白质导向分泌途径、线粒体和叶绿体的著名N端序列基序的特性，并简述了基于这些分选信号和其他序列特性预测亚细胞定位的方法的简要历史。然后，我们概述了如何使用一些可通过互联网访问的工具来获得对真核和原核蛋白质可靠的亚细胞定位预测。特别是，我们提供了基于氨基酸序列的预测工具TargetP、SignalP、ChloroP和TMHMM联合使用的详细分步说明，这些工具都托管在丹麦技术大学生物序列分析中心。此外，我们描述并提供了其他有用的亚细胞定位预测工具的网络参考。最后，我们一般地讨论预测性能指标，特别是TargetP和SignalP的性能。
