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SignalP and TMHMM

The SignalP and TMHMM plugin contains tools for finding secretory signal peptides and predicting transmembrane helices in protein sequences.

This plugin contains two tools: Signal Peptide Prediction and Transmembrane Helix Prediction. When installed, these tools are placed in the Toolbox under the Protein Analyses folder.

An active internet connection is required to run these tools.

Signal Peptide Prediction

Signal peptides target proteins to the extracellular environment either through direct plasmamembrane translocation in prokaryotes or are 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-NN [Nielsen et al., 1997] [Bendtsen et al., 2004a] located at https://services.healthtech.dtu.dk/service.php?SignalP-4.1.

Predicted signal peptides can automatically be added to the sequence as annotations or predictions can be viewed in text.

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. This score has been shown to be the most accurate [Klee and Ellis, 2005] in an evaluation study of signal peptide predictors.

These organisms can be selected:

  • Eukaryote
  • Gram-negative bacteria
  • Gram-positive bacteria

The predictions obtained can be shown as annotations on the sequence. Tabular output and the detailed text output from SignalP can also be generated. Each annotation carries a tooltip note saying that the corresponding annotation was predicted using SignalP.

You can perform the analysis on several protein sequences at a time. This will add annotations to all the sequences and open a view for each sequence if a signal peptide is found.

Additional information on SignalP can be found at https://services.healthtech.dtu.dk/service.php?SignalP-4.1 and in the original research paper [Nielsen et al., 1997] [Bendtsen et al., 2004a].

Transmembrane Helix Prediction

To predict transmembrane helixes, simply select the sequences of interest and launch the Transmembrane Helix Prediction tool.

After running the prediction, the protein sequence will show predicted transmembrane helices as annotations on the original sequence. Annotations showing the topology, which parts of the proteins are located on the inside or on the outside, will also be shown. Tabular output and the detailed text output from TMHMM can also be generated.

This tool uses TMHMM version 2.0, located at: https://services.healthtech.dtu.dk/service.php?TMHMM-2.0. A tooltip is associated with each annotation with a note field recording that the prediction was carried out using TMHMM 2.0.

Additional information about SignalP and TMHMM can be found at https://services.healthtech.dtu.dk.



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Platform support



QIAGEN CLC Genomics Workbench

 [23.9.9, 23.0.4, 23.0.3, 23.0.1, 23.0]

QIAGEN CLC Main Workbench

 [23.0.2, 23.0.1, 23.0]


QIAGEN CLC Genomics Workbench

 [22.0.3, 22.0.2, 22.0.1, 22.0]

QIAGEN CLC Main Workbench

 [22.0.3, 22.0.2, 22.0.1, 22.0]


QIAGEN CLC Genomics Workbench

 [21.0.6, 21.0.5, 21.0.4, 21.0.3, 21.0.2, 21.0.1, 21.0]

QIAGEN CLC Main Workbench

 [21.0.6, 21.0.5, 21.0.4, 21.0.3, 21.0.2, 21.0.1, 21.0]


QIAGEN CLC Genomics Workbench

 [20.0.5, 20.0.4, 20.0.3, 20.0.2, 20.0.1, 20.0]

QIAGEN CLC Main Workbench

 [20.0.5, 20.0.4, 20.0.3, 20.0.2, 20.0.1, 20.0]

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