BactPepDB

BactGeneSHOW

P. Nicolas, L. Bize, M. Hoebeke, F. Rodolphe, S. D. Ehrlich, B. Prum & P. Bessières.
Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models.
Nucleic Acids Res. 2002 March 15; 30(6): 1418-1426.

DIpro 2.0

J. Cheng, H. Saigo, & P. Baldi.
Large-Scale Prediction of Disulphide Bridges Using Kernel Methods, Two-Dimensional Recursive Neural Networks, and Weighted Graph Matching.
Proteins, vol. 62, no. 3, pp. 617-629, (2006)

Psipred

D.T. Jones
Protein secondary structure prediction based on position-specific scoring matrices.
J. Mol. Biol. 292:195-202.(1999)

SignalP 4.1

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

TMHMM 2.0

A. Krogh, B. Larsson, G. von Heijne, and E. L. L. Sonnhammer.
Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes.
Journal of Molecular Biology, 305(3):567-580, January 2001.

E. L.L. Sonnhammer, G. von Heijne, and A. Krogh.
A hidden Markov model for predicting transmembrane helices in protein sequences.
In J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen, editors, Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, pages 175-182, Menlo Park, CA, 1998. AAAI Press.