ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites.
Reads0
Chats0
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
Citations
More filters
Journal ArticleDOI
Analysis of carotenoid biosynthetic gene expression during marigold petal development.
TL;DR: Cloned genes encoding early steps in the biosynthesis of isopentenyl pyrophosphate, the precursor of all isoprenoids, including carotenoids, as well as two genes required for plastid division are examined.
Journal ArticleDOI
Downregulation of a chloroplast-targeted beta-amylase leads to a starch-excess phenotype in leaves.
TL;DR: For the first time, a physiological role for a beta-amylase in plants has been demonstrated and it was shown that the antisense plants degraded only 8-30% of their total starch, in comparison with 50% in the wild type, over the dark period.
Journal ArticleDOI
Pentatricopeptide Repeat Proteins with the DYW Motif Have Distinct Molecular Functions in RNA Editing and RNA Cleavage in Arabidopsis Chloroplasts
Kenji Okuda,Anne Laure Chateigner-Boutin,Takahiro Nakamura,Takahiro Nakamura,Etienne Delannoy,Mamoru Sugita,Fumiyoshi Myouga,Reiko Motohashi,Kazuo Shinozaki,Ian Small,Toshiharu Shikanai +10 more
TL;DR: It is proposed that different DYW family members have acquired distinct functions in the divergent processes of RNA maturation, including RNA cleavage and RNA editing.
Journal ArticleDOI
A Chromoplast-Specific Carotenoid Biosynthesis Pathway Is Revealed by Cloning of the Tomato white-flower Locus
TL;DR: It is hypothesized that this carotenoid biosynthesis pathway in tomato was initially selected during evolution to enhance flower coloration and only later recruited to enhance fruit pigmentation.
Journal ArticleDOI
A phosphatidic acid-binding protein of the chloroplast inner envelope membrane involved in lipid trafficking
TL;DR: It is proposed that TGD2 represents the substrate-binding or regulatory component of a phosphatidic acid/lipid transport complex in the chloroplast inner envelope membrane.
References
More filters
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.
Related Papers (5)
Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana
Steven J. Clough,Andrew F. Bent +1 more