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Locating proteins in the cell using TargetP, SignalP and related tools

Abstract

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.

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Figure 1
Figure 2: Output from the TargetP server, tested on ten sequences from Arabidopsis thaliana.
Figure 3
Figure 4: The graphical output of SignalP-NN, showing C-, S- and Y-score.
Figure 5: The graphical output of SignalP-HMM, showing the posterior probabilities for n-, h- and c-region and cleavage site.
Figure 6: The graphical output of TMHMM, showing the posterior probabilities for transmembrane, inside (i.e., cytoplasmic), and outside (i.e., lumenal or exterior) regions.

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Correspondence to Henrik Nielsen.

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This protocol describes a number of prediction programs hosted by the Center for Biological Sequence Analysis, Technical University of Denmark, developed, in part or in total, by the authors themselves. The Internet-accessible versions of these programs are free for all users. However, the downloadable versions (for local use) have been commercialised by the Technical University of Denmark. They are free for academic users but are provided for a fee to commercial users. The revenue from these commercial sales is divided between the program developers and the Technical University of Denmark, where two of the authors (S.B. and H.N.) are employed.

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Emanuelsson, O., Brunak, S., von Heijne, G. et al. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2, 953–971 (2007). https://doi.org/10.1038/nprot.2007.131

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