ChloroP, a neural network‐based method for predicting chloroplast transit peptides and their cleavage sites
- 1 January 1999
- journal article
- Published by Wiley in Protein Science
- Vol. 8 (5), 978-984
- https://doi.org/10.1110/ps.8.5.978
Abstract
We present a neural network based method (ChloroP) for identifying chloroplast transit peptides and their cleavage sites. Using cross-validation, 88% of the sequences in our homology reduced training set were correctly classified as transit peptides or nontransit peptides. This performance level is well above that of the publicly available chloroplast localization predictor PSORT. Cleavage sites are predicted using a scoring matrix derived by an automatic motif-finding algorithm. Approximately 60% of the known cleavage sites in our sequence collection were predicted to within +/-2 residues from the cleavage sites given in SWISS-PROT. An analysis of 715 Arabidopsis thaliana sequences from SWISS-PROT suggests that the ChloroP method should be useful for the identification of putative transit peptides in genome-wide sequence data. The ChloroP predictor is available as a web-server at http://www.cbs.dtu.dk/services/ChloroP/.Keywords
This publication has 29 references indexed in Scilit:
- A Single Precursor Protein for Ferrochelatase-I fromArabidopsis Is Imported in Vitro into Both Chloroplasts and MitochondriaPublished by Elsevier BV ,1997
- Issues in searching molecular sequence databasesNature Genetics, 1994
- Selection of representative protein data setsProtein Science, 1992
- Prediction of human mRNA donor and acceptor sites from the DNA sequenceJournal of Molecular Biology, 1991
- The signal peptideThe Journal of Membrane Biology, 1990
- A conserved cleavage‐site motif in chloroplast transit peptidesFEBS Letters, 1990
- Sequence logos: a new way to display consensus sequencesNucleic Acids Research, 1990
- Domain structure of mitochondrial and chloroplast targeting peptidesJBIC Journal of Biological Inorganic Chemistry, 1989
- Predicting the secondary structure of globular proteins using neural network modelsJournal of Molecular Biology, 1988
- Transport of proteins into chloroplastsJBIC Journal of Biological Inorganic Chemistry, 1984