Signal peptides target proteins to the extracellular environment either through direct plasmamembrane translocation in prokaryotes or is routed through the Endoplasmatic Reticulum in eukaryotic cells. The signal peptide is removed from the resulting mature protein during translocation across the membrane. For prediction of signal peptides, we query SignalP [Nielsen et al., 1997,Bendtsen et al., 2004b] located at http://www.cbs.dtu.dk/services/SignalP/. Thus an active internet connection is required to run the signal peptide prediction. Additional information on SignalP and Center for Biological Sequence analysis (CBS) can be found at http://www.cbs.dtu.dk and in the original research papers [Nielsen et al., 1997,Bendtsen et al., 2004b].
In order to predict potential signal peptides of proteins, the D-score from the SignalP output is used for discrimination of signal peptide versus non-signal peptide (see section 16.1.3). This score has been shown to be the most accurate [Klee and Ellis, 2005] in an evaluation study of signal peptide predictors.
In order to use SignalP, you need to download the SignalP plug-in using the plug-in manager.
When the plug-in is downloaded and installed, you can use it to predict signal peptides:
Select a protein sequence | Toolbox in the Menu Bar | Classical Sequence Analysis () | Protein Analysis ()| Signal Peptide Prediction ()
or right-click a protein sequence | Toolbox | Classical Sequence Analysis () | Protein Analysis ()| Signal Peptide Prediction ()
If a sequence was selected before choosing the Toolbox action, this sequence is now listed in the Selected Elements window of the dialog. Use the arrows to add or remove sequences or sequence lists from the selected elements.
Click Next to set parameters for the SignalP analysis.