ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites.
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TLDR
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.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/.read more
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References
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Journal ArticleDOI
A mathematical theory of communication
TL;DR: This final installment of the paper considers the case where the signals or the messages or both are continuously variable, in contrast with the discrete nature assumed until now.
Book ChapterDOI
Learning internal representations by error propagation
TL;DR: This chapter contains sections titled: The Problem, The Generalized Delta Rule, Simulation Results, Some Further Generalizations, Conclusion.
MonographDOI
Parallel Distributed Processing: Explorations in the Microstructure of Cognition: Foundations
Journal ArticleDOI
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
TL;DR: A new method for the identification of signal peptides and their cleavage sites based on neural networks trained on separate sets of prokaryotic and eukaryotic sequence that performs significantly better than previous prediction schemes and can easily be applied on genome-wide data sets.
SHORT COMMUNICATION Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
TL;DR: In this paper, a new method for the identification of in performance compared with the weight matrix method signal peptides and their cleavage sites based on neural (Arrigo et al., 1991; Ladunga et al, 1991; Schneider and networks trained on separate sets of prokaryotic and eukaryotic sequence.
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