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SignalP 4.1 Server

SignalP 4.1 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. Most of the previous versions are available online, for comparison and reference.

NEW (August 2017): A book chapter on SignalP 4.1 has been published:

Predicting Secretory Proteins with SignalP
Henrik Nielsen
In Kihara, D (ed): Protein Function Prediction (Methods in Molecular Biology vol. 1611) pp. 59-73, Springer 2017.
doi: 10.1007/978-1-4939-7015-5_6
PMID: 28451972

NOTE (added May 2018): Remember, the presence or absence of a signal peptide is not the whole story about the localization of a protein!
If you want to find out more about the sorting of your eukaryotic proteins, try the protein subcellular localization predictor DeepLoc.

FAQ Article abstracts Instructions Output format Performance 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 (explain)
Gram-negative bacteria
Gram-positive bacteria
D-cutoff values (explain)
Default (optimized for correlation)
Sensitive (reproduce SignalP 3.0's sensitivity)
User defined:
D-cutoff for SignalP-noTM networks
D-cutoff for SignalP-TM networks
Graphics output (explain)
No graphics
PNG (inline)
PNG (inline) and EPS (as links)
Output format (explain)
Short (no graphics)
All - SignalP-noTM and SignalP-TM output (no graphics)
Method (explain)
Input sequences may include TM regions
Input sequences do not include TM regions
Positional limits (explain)
Minimal predicted signal peptide length. Default: 10
N-terminal truncation of input sequence (0 means no truncation).
Default: Truncate sequence to a length of 70 aa

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
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 4.1 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 (Darwin), Windows (Cygwin), 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: