PrediSi: prediction of signal peptides and their cleavage positions

We have developed PrediSi (Prediction of Signal peptides), a new tool for predicting signal peptide sequences and their cleavage positions in bacterial and eukaryotic amino acid sequences. In contrast to previous prediction tools, our new software is especially useful for the analysis of large datasets in real time with high accuracy. PrediSi allows the evaluation of whole proteome datasets, which are currently accumulating as a result of numerous genome projects and proteomics experiments. The method employed is based on a position weight matrix approach improved by a frequency correction which takes in to consideration the amino acid bias present in proteins. The software was trained using sequences extracted from the most recent version of the SwissProt database. PrediSi is accessible via a web interface. An extra Java package was designed for the integration of PrediSi into other software projects. The tool is freely available on the World Wide Web at http://www.predisi.de.

[1]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[2]  S. Bron,et al.  Signal Peptide-Dependent Protein Transport inBacillus subtilis: a Genome-Based Survey of the Secretome , 2000, Microbiology and Molecular Biology Reviews.

[3]  T. D. Schneider,et al.  Sequence logos: a new way to display consensus sequences. , 1990, Nucleic acids research.

[4]  S. Brunak,et al.  SHORT COMMUNICATION Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites , 1997 .

[5]  G von Heijne,et al.  Signal sequences. The limits of variation. , 1985, Journal of molecular biology.

[6]  S. Brunak,et al.  Defining a similarity threshold for a functional protein sequence pattern: The signal peptide cleavage site , 1996, Proteins.

[7]  Lila M Gierasch,et al.  Signal Sequences: The Same Yet Different , 1996, Cell.

[8]  Dieter Jahn,et al.  JVirGel: calculation of virtual two-dimensional protein gels , 2003, Nucleic Acids Res..

[9]  Anders Krogh,et al.  Prediction of Signal Peptides and Signal Anchors by a Hidden Markov Model , 1998, ISMB.

[10]  T A Rapoport,et al.  Protein transport across the eukaryotic endoplasmic reticulum and bacterial inner membranes. , 1996, Annual review of biochemistry.

[11]  Rolf Apweiler,et al.  A comparison of signal sequence prediction methods using a test set of signal peptides , 2000, Bioinform..

[12]  Chris M. Brown,et al.  Compensation for nucleotide bias in a genome by representation as a discrete channel with noise , 2002, Bioinform..