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
The nucleobase cation symporter 1 of Chlamydomonas reinhardtii and that of the evolutionarily distant Arabidopsis thaliana display parallel function and establish a plant-specific solute transport profile
TL;DR: The results suggest that the solute specificity for plant NCS1 occurred early in plant evolution and are distinct from solute transport specificities of single cell fungal N CS1 proteins.
Journal ArticleDOI
Tailored biosynthesis of gibberellin plant hormones in yeast.
Kanchana Rueksomtawin Kildegaard,Jonathan A. Arnesen,Belén Adiego-Pérez,Daniela Rago,Mette Kristensen,Andreas Klitgaard,Esben Halkjaer Hansen,Jørgen Hansen,Irina Borodina +8 more
TL;DR: In this paper, the authors explored the potential of the oleaginous yeast Yarrowia lipolytica to produce specific profiles of GAs, which can increase the productivity and quality of many vegetable and fruit crops.
Journal ArticleDOI
Isolation and functional analysis of two Cistus creticus cDNAs encoding geranylgeranyl diphosphate synthase.
TL;DR: This work is the first attempt to study the terpenoid biosynthesis at the molecular level in C. creticus, andGene and protein expression analyses suggest that this enzyme is developmentally and tissue-regulated showing maximum expression in trichomes and smallest leaves.
Journal ArticleDOI
Susceptibility to Verticillium longisporum is linked to monoterpene production by TPS23/27 in Arabidopsis
TL;DR: Results show that TPS23/27-produced monoterpenes stimulate germination and subsequent invasion of V. longisporum in Arabidopsis roots and significantly altered levels of all identified TPS 23/27 monoterpene products were significantly altered in the transgenic plants.
Journal ArticleDOI
Rhomboid proteases in plants - still in square one?
Ronit Rimon Knopf,Zach Adam +1 more
TL;DR: The current knowledge in the rhomboid field in general, and in plant rhomboids in particular, is presented and possible physiological roles of different plantrhomboids are discussed.
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