ChloroP, a neural network‐based method for predicting chloroplast transit peptides and their cleavage sites

ChloroP, a neural network‐based method for predicting chloroplast transit peptides and their... 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 62 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/. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Protein Science Wiley

ChloroP, a neural network‐based method for predicting chloroplast transit peptides and their cleavage sites

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Publisher
Wiley
Copyright
Copyright © 1999 The Protein Society
ISSN
0961-8368
eISSN
1469-896X
D.O.I.
10.1110/ps.8.5.978
Publisher site
See Article on Publisher Site

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 62 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/.

Journal

Protein ScienceWiley

Published: Jan 1, 1999

References

  • Simultaneous targeting of pea glutathione reductase and of a bacterial fusion protein to chloroplasts and mitochondria in transgenic tobacco
    Creissen, Creissen; Reynolds, Reynolds; Xue, Xue; Mullineaux, Mullineaux
  • Selection of representative protein data sets
    Hobohm, Hobohm; Scharf, Scharf; Schneider, Schneider; Sander, Sander
  • Feature‐extraction from endopeptidase cleavage sites in mitochondrial targeting peptides
    Schneider, Schneider; Sjöling, Sjöling; Wallin, Wallin; Wrede, Wrede; Glazier, Glazier; von Heijne, von Heijne
  • Protein translocation into and across the chloroplastic envelope membranes
    Soll, Soll; Tien, Tien

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