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SignalP 4.0: discriminating signal peptides from transmembrane regions

Nature Methods volume 8, pages 785–786 (2011)Cite this article

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To the Editor:

The secretory signal peptide is a ubiquitous protein-sorting signal that targets its passenger protein for translocation across the endoplasmic reticulum membrane in eukaryotes and the cytoplasmic membrane in prokaryotes1. Many methods have been published for predicting signal peptides from the amino acid sequence, including SignalP2,3,4, PrediSi5, SPEPlip6, Signal-CF7, Signal-3L8 and Signal-BLAST9. A benchmark study done in 2009 found SignalP 3.0 to be the best method10.

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Figure 1: Comparison of signal peptide prediction algorithm performance shown as the Matthews correlation coefficient for eukaryotes, Gram-positive bacteria and Gram-negative bacteria.

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Authors and Affiliations

  1. Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark

    Thomas Nordahl Petersen, Søren Brunak & Henrik Nielsen

  2. Novo Nordisk Foundation Center for Protein Research, Health Sciences Faculty, University of Copenhagen, Copenhagen, Denmark

    Søren Brunak

  3. Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden

    Gunnar von Heijne

  4. Science for Life Laboratory, Stockholm University, Solna, Sweden

    Gunnar von Heijne

Authors
  1. Thomas Nordahl Petersen
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  2. Søren Brunak
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  3. Gunnar von Heijne
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  4. Henrik Nielsen
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Correspondence to Henrik Nielsen.

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Competing interests

The downloadable version of SignalP 4.0 (for local use) has been commercialized by the Technical University of Denmark. (It is provided for a fee to commercial users.) The revenue from these commercial sales is divided between the program developers (T.N.P., S.B., G.v.H. and H.N.) and the Technical University of Denmark, where T.N.P., S.B. and H.N. are employed.

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Petersen, T., Brunak, S., von Heijne, G. et al. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8, 785–786 (2011). https://doi.org/10.1038/nmeth.1701

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