2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2016
Abstrakt

Olof Emanuelsson, Soren Brunak, Gunnar von Heijne, Henrik Nielsen. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc, 2(4):953-961. 2007.

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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.