Signal Peptide Prediction

Signal peptide identification, like DNA intron/exon sequence discrimination, involves the two related problems of signal peptide discrimination (search for content) and cleavage site recognition (search for signal). It is well suited to neural network methods for several reasons. The functional units are encoded by local, linear sequences of amino acids rather than global 3-dimensional structures (Claros et al., 1997). The ambiguity of 

C-scores are considered. The system has been applied to complete genomic sequence analysis and is currently considered as the standard method for signal peptide prediction. On-line prediction is available from the WWW server at http //www.cbs.dtu.dk. 

Cleavage Site Feature Extraction and Peptide Design 

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Ladunga, I., Czako, F., Csabai, I., and Geszti, T. (1991). Improving signal peptide prediction accuracy by simulated neural network. Comput. Appl. Biosci. 7, 485-487. Landolt-Marticorena, C., Williams, K., Deber, C., and Reithmeier, R. (1993). Non-random distribution of amino acids in the ransmembrane segments of human type I single span membrane proteins. J. Mol. Biol. 229, 602-608. 

Organism Type of protease Gene Length ofORF (bp) Length of deduced amino acid sequence Length of putative signal peptide Predicted properties of the protein Length Calculated Calculated Mw (kDa) pi Reference... 

Ladungaer al., 1991 Signal Peptide Prediction 4L/FF/Tiling BIN20/1(Y,N)... 

Neural network applications for protein sequence analysis are summarized in Table 11.1. Like the DNA coding region recognition problem, signal peptide prediction (11.2) involves both search for content and search for signal tasks. An effective means for protein sequence analysis is reverse database searching to detect functional motifs or sites (11.3) and identify protein families (11.4). Most of the functional motifs are also... 

Ladunga, I., Czako, F., Csabai, I. Geszti, T. (1991). Improving signal peptide prediction accuracy by simulated neural network. ComputAppl Biosci 7,485-7. 

Kail, I., A. Krogh, and E. L. L. Sonnhammer. 2004. A combined transmembrane topology and signal peptide prediction method. J Mol Biol 338 1027-36. 

Figure 17.4. This script reformats a set of neuron-related C. elegans genes for submission to the SignalP signal peptide prediction program.

Antelmann, H. et al (2001) A proteomic view on genome-based signal peptide predictions. Genome Res.,... 

Kail L, Krogh A, Sonnhammer ELL. Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server. Nucl Acids Res. 2007b 35 Suppl 2 W429-32. doi 10.1093/nar/gkm256. 

SignalP (http //www.cbs.dtu.dk/services/SignalP), site of the Center for Biological Sequence Analisys (CBS) for prediction of the presence and location of signal peptides in given amino acid sequences. 

Because the basic structure of signal peptides is common between bacteria and eukaryotes, all prediction methods can be applied to each category of data although the differences of the optimized, numeric parameters exist. Certainly, a method with high accuracy would be desirable for practical uses. However, it is difficult to compare the perfor-... 

McGeoch, D. (1985). On the predictive recognition of signal peptide sequences. Virus Res. 3, 271-286. 

Nakai, K. (1996). Refinement of the prediction methods of signal peptides for the genome analyses of Saccharomyces cerevisiae and Bacillus subtilis. In Akutsa, T., Asai, K., Hagiya, M., Kuhara, S., Miyano, S., andNakai, K. (eds.) Genome Informatics 1996 Universal Academy Press, Inc., Tokyo, Japan, 72-81. 

Nielsen, H., Brunak, S., and von Heijne, G. (1999). Machine learning approaches for the prediction of signal peptides and other protein sorting signals. PmteinEng. 12,3—9. 

Nielsen, H., and Krogh, A. (1998). Prediction of signal peptides and signal anchors by a hidden Markov model. InteU. Sysl. Mol. Biol. 6, 122-130. 

Fig. 9 Alignment of the amino acid sequences of pheromone-binding proteins from the silkworm moth B. mori and the cockroach L. maderae, BmorPBP and LmadPBP,respectively and a putative odorant-binding protein from D. melanogaster, LUSH. In LmadPBP and LUSH the N-terminal sequence of the mature proteins were predicted by cleaving signal peptides in silico [28,79], whereas in BmorPBP this was confirmed by the sequence of the isolated protein [38]...

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