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SignalP 3.0 Server

SignalP 3.0 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 and hidden Markov models.

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

NOTE: This is not the newest version of SignalP. To use the current version, please go to

Background Article abstracts Instructions Output format


Paste a single 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
Neural networks
Hidden Markov models
No graphics
GIF (inline)
GIF (inline) and EPS (as links)

Output format
Short (no graphics!)

Truncate each sequence to max. residues.

We recommend that only the N-terminal part of each protein sequence is submitted.
Enter 0 (zero) to disable 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:

  • Current version:

    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.

  • Original paper:

    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.

  • If you specifically use the SignalP-HMM output, please also cite:

    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.

  • A 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).

    is available for download - please click here to access the paper and supplementary materials.


Would you prefer to run SignalP at your own site? SignalP 3.0 is available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms. There is a download page for academic users where you can get the newest SignalP version; if you specifically want the 3.0 version, please send a mail to Support. Non-academic users are requested to contact CBS Software Package Manager at


Scientific problems:        Technical problems: