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SignalP 4.0 Server

SignalP 4.0 server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.

View the version history of this server. All the previous versions are available on line, for comparison and reference.

New: ePrint of the SignalP 4.0 paper is available, see Citations.

Background Article abstracts Instructions Output format Data


Paste a single amino acid sequence or several sequences in FASTA format into the field below:

Submit a file in FASTA format directly from your local disk:

Organism group
Gram-negative bacteria
Gram-positive bacteria
Input sequences may include TM regions
Input sequences do not include TM regions
No graphics
PNG (inline)
PNG (inline) and EPS (as links)

Output format
Short (no graphics)
All - SignalP-noTM and SignalP-TM output (no graphics)

Optional - User defined D-cutoff values (default scores)
D-cutoff for SignalP-noTM networks
D-cutoff for SignalP-TM networks

Truncate sequence
Default: Truncate sequence to a length of 70 aa - 0 means no truncation

At most 2,000 sequences and 200,000 amino acids per submission; each sequence not more than 6,000 amino acids.

The sequences are kept confidential and will be deleted after processing.


For publication of results, please cite:

SignalP 4.0: discriminating signal peptides from transmembrane regions
Thomas Nordahl Petersen, Søren Brunak, Gunnar von Heijne & Henrik Nielsen
Nature Methods, 8:785-786, 2011

PMID: 21959131
Access to the paper: if you have a personal or institutional subscription to Nature Methods, use the doi: link above. If not, use the ePrint link below:
View ePrint in a popup window
Access to the supplementary materials: nmeth.1701-S1.pdf

Other relevant papers:

  • Original paper (version 1.0):

    Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
    Henrik Nielsen, Jacob Engelbrecht, Søren Brunak and Gunnar von Heijne.
    Protein Engineering, 10:1-6, 1997.

    View the abstract.

  • SignalP-HMM (version 2.0):

    Prediction of signal peptides and signal anchors by a hidden Markov model.
    Henrik Nielsen and Anders Krogh.
    Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB 6),
    AAAI Press, Menlo Park, California, pp. 122-130, 1998.

    View the abstract.

  • Version 3.0:

    Improved prediction of signal peptides: SignalP 3.0.
    Jannick Dyrløv Bendtsen, Henrik Nielsen, Gunnar von Heijne and Søren Brunak.
    J. Mol. Biol., 340:783-795, 2004.

    View the abstract.         Download the full article in PDF.

  • Paper about using SignalP and other protein subcellular localization prediction methods:

    Locating proteins in the cell using TargetP, SignalP, and related tools
    Olof Emanuelsson, Søren Brunak, Gunnar von Heijne, Henrik Nielsen
    Nature Protocols 2:953-971 (2007).

    Access the paper and supplementary materials.


Would you prefer to run SignalP at your own site? SignalP 4.0 is available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for Mac OS X and the most common UNIX platforms. There is a download page for academic users; other users are requested to contact CBS Software Package Manager at


Scientific problems:        Technical problems: