SignalP 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.
Lukas Käll, Anders Krogh and Erik L. L. Sonnhammer.
A Combined Transmembrane Topology and Signal Peptide Prediction Method.
Journal of Molecular Biology, 338(5):1027-1036, May 2004.
PolyPhobius is described in:
Lukas Käll, Anders Krogh and Erik Sonnhammer.
An HMM posterior decoder for sequence feature prediction that includes homology information
Bioinformatics, 21 (Suppl 1):i251-i257, June 2005.
SPEPlip is a neural network-based method, trained and tested on a set of experimentally derived signal peptides from eukaryotes and prokaryotes. SPEPlip identifies the presence of sorting signals and predicts their cleavage sites.