Protein Engineering, Vol. 12, No. 1, 3-9,
January 1999
© 1999 Oxford University Press
REVIEW |
Machine learning approaches for the prediction of signal peptides and other protein sorting signals
Center for Biological Sequence Analysis Department of Biotechnology, The Technical University of Denmark, DK-2800 Lyngby, Denmark and 2 Department of Biochemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
Prediction of protein sorting signals from the sequence of amino acids has great importance in the field of proteomics today. Recently, the growth of protein databases, combined with machine learning approaches, such as neural networks and hidden Markov models, have made it possible to achieve a level of reliability where practical use in, for example automatic database annotation is feasible. In this review, we concentrate on the present status and future perspectives of SignalP, our neural network-based method for prediction of the most well-known sorting signal: the secretory signal peptide. We discuss the problems associated with the use of SignalP on genomic sequences, showing that signal peptide prediction will improve further if integrated with predictions of start codons and transmembrane helices. As a step towards this goal, a hidden Markov model version of SignalP has been developed, making it possible to discriminate between cleaved signal peptides and uncleaved signal anchors. Furthermore, we show how SignalP can be used to characterize putative signal peptides from an archaeon, Methanococcus jannaschii. Finally, we briefly review a few methods for predicting other protein sorting signals and discuss the future of protein sorting prediction in general.
1 To whom correspondence should be addressed
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T. Collins, M.-A. Meuwis, I. Stals, M. Claeyssens, G. Feller, and C. Gerday A Novel Family 8 Xylanase, Functional and Physicochemical Characterization J. Biol. Chem., September 13, 2002; 277(38): 35133 - 35139. [Abstract] [Full Text] [PDF]
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D. A. Shagin, E. V. Barsova, E. A. Bogdanova, O. V. Britanova, N. G. Gurskaya, K. A. Lukyanov, M. V. Matz, N. I. Punkova, N. Y. Usman, E. P. Kopantzev, et al. Identification and characterization of a new family of C-type lectin-like genes from planaria Girardia tigrina Glycobiology, August 1, 2002; 12(8): 463 - 472. [Abstract] [Full Text] [PDF]
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P. Mallick, D. R. Boutz, D. Eisenberg, and T. O. Yeates Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds PNAS, July 23, 2002; 99(15): 9679 - 9684. [Abstract] [Full Text] [PDF]
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Y.-Y. Chen, K. J. Cross, R. A. Paolini, J. E. Fielding, N. Slakeski, and E. C. Reynolds CPG70 Is a Novel Basic Metallocarboxypeptidase with C-terminal Polycystic Kidney Disease Domains from Porphyromonas gingivalis J. Biol. Chem., June 21, 2002; 277(26): 23433 - 23440. [Abstract] [Full Text] [PDF]
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A. J. Sanchez, M. J. Vincent, and S. T. Nichol Characterization of the Glycoproteins of Crimean-Congo Hemorrhagic Fever Virus J. Virol., June 14, 2002; 76(14): 7263 - 7275. [Abstract] [Full Text] [PDF]
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C. Biondo, C. Beninati, D. Delfino, M. Oggioni, G. Mancuso, A. Midiri, M. Bombaci, G. Tomaselli, and G. Teti Identification and Cloning of a Cryptococcal Deacetylase That Produces Protective Immune Responses Infect. Immun., May 1, 2002; 70(5): 2383 - 2391. [Abstract] [Full Text] [PDF]
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Q. Bao, Y. Tian, W. Li, Z. Xu, Z. Xuan, S. Hu, W. Dong, J. Yang, Y. Chen, Y. Xue, et al. A Complete Sequence of the T. tengcongensis Genome Genome Res., May 1, 2002; 12(5): 689 - 700. [Abstract] [Full Text] [PDF]
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M. Schubert, U. A. Petersson, B. J. Haas, C. Funk, W. P. Schroder, and T. Kieselbach Proteome Map of the Chloroplast Lumen of Arabidopsis thaliana J. Biol. Chem., March 1, 2002; 277(10): 8354 - 8365. [Abstract] [Full Text] [PDF]
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A. Bateman, E. Birney, L. Cerruti, R. Durbin, L. Etwiller, S. R. Eddy, S. Griffiths-Jones, K. L. Howe, M. Marshall, and E. L. L. Sonnhammer The Pfam Protein Families Database Nucleic Acids Res., January 1, 2002; 30(1): 276 - 280. [Abstract] [Full Text] [PDF]
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Y. Fan, C. Y. Wu, C. W. Chen, T. W. Chang, and C. Lim Preparing a human membrane and secreted protein-enriched cDNA library using PCR primers derived from a genomic database Nucleic Acids Res., November 15, 2001; 29(22): e114 - e114. [Abstract] [Full Text] [PDF]
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Y. Hashimoto, T. Niikura, H. Tajima, T. Yasukawa, H. Sudo, Y. Ito, Y. Kita, M. Kawasumi, K. Kouyama, M. Doyu, et al. A rescue factor abolishing neuronal cell death by a wide spectrum of familial Alzheimer's disease genes and Abeta PNAS, May 22, 2001; 98(11): 6336 - 6341. [Abstract] [Full Text] [PDF]
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B. S. Davis, G.-J. J. Chang, B. Cropp, J. T. Roehrig, D. A. Martin, C. J. Mitchell, R. Bowen, and M. L. Bunning West Nile Virus Recombinant DNA Vaccine Protects Mouse and Horse from Virus Challenge and Expresses In Vitro a Noninfectious Recombinant Antigen That Can Be Used in Enzyme-Linked Immunosorbent Assays J. Virol., May 1, 2001; 75(9): 4040 - 4047. [Abstract] [Full Text]
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M. Göttfert, S. Röthlisberger, C. Kündig, C. Beck, R. Marty, and H. Hennecke Potential Symbiosis-Specific Genes Uncovered by Sequencing a 410-Kilobase DNA Region of the Bradyrhizobium japonicum Chromosome J. Bacteriol., February 15, 2001; 183(4): 1405 - 1412. [Abstract] [Full Text]
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K.-C. Chou Using subsite coupling to predict signal peptides Protein Eng. Des. Sel., February 1, 2001; 14(2): 75 - 79. [Abstract] [Full Text] [PDF]
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B. Eisenhaber, P. Bork, and F. Eisenhaber Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes Protein Eng. Des. Sel., January 1, 2001; 14(1): 17 - 25. [Abstract] [Full Text] [PDF]
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M. Frisardi, S. K. Ghosh, J. Field, K. Van Dellen, R. Rogers, P. Robbins, and J. Samuelson The Most Abundant Glycoprotein of Amebic Cyst Walls (Jacob) Is a Lectin with Five Cys-Rich, Chitin-Binding Domains Infect. Immun., July 1, 2000; 68(7): 4217 - 4224. [Abstract] [Full Text] [PDF]
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P. Bork Powers and Pitfalls in Sequence Analysis: The 70% Hurdle Genome Res., April 1, 2000; 10(4): 398 - 400. [Full Text]
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J.-M. Revest, L. DeMoerlooze, and C. Dickson Fibroblast Growth Factor 9 Secretion Is Mediated by a Non-cleaved Amino-terminal Signal Sequence J. Biol. Chem., March 10, 2000; 275(11): 8083 - 8090. [Abstract] [Full Text] [PDF]
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K. Hanasaki, T. Ono, A. Saiga, Y. Morioka, M. Ikeda, K. Kawamoto, K.-i. Higashino, K. Nakano, K. Yamada, J. Ishizaki, et al. Purified Group X Secretory Phospholipase A2 Induced Prominent Release of Arachidonic Acid from Human Myeloid Leukemia Cells J. Biol. Chem., November 26, 1999; 274(48): 34203 - 34211. [Abstract] [Full Text] [PDF]
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N. Xu and B. Dahlback A Novel Human Apolipoprotein (apoM) J. Biol. Chem., October 29, 1999; 274(44): 31286 - 31290. [Abstract] [Full Text] [PDF]
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J. D. H. Jongbloed, U. Martin, H. Antelmann, M. Hecker, H. Tjalsma, G. Venema, S. Bron, J. M. van Dijl, and J. Muller TatC Is a Specificity Determinant for Protein Secretion via the Twin-arginine Translocation Pathway J. Biol. Chem., December 22, 2000; 275(52): 41350 - 41357. [Abstract] [Full Text] [PDF]
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