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
Characterization of homogentisate prenyltransferases involved in plastoquinone-9 and tocochromanol biosynthesis.
TL;DR: Functional expression studies in Escherichia coli revealed that the enzyme possessed properties similar to the prenyltransferase of Arabidopsis thaliana encoded by At3g11950 but different from the phytyltransferases of A.Thaliana, providing evidence that the latter represent homogentisate solanesyltransferases involved in plastoquinone‐9 biosynthesis.
Journal ArticleDOI
A nucleus-encoded maize protein with sigma factor activity accumulates in mitochondria and chloroplasts.
Thomas A. Beardslee,Sanchita Roy-Chowdhury,Pankaj Jaiswal,Laurence Buhot,Silva Lerbs-Mache,David B. Stern,Lori A. Allison +6 more
TL;DR: ZmSig2B is an unusual nucleus-encoded sigma factor that appears to function in both chloroplasts and mitochondria and is supported by its presence in a maize mitochondrial transcription extract.
Journal ArticleDOI
RAP, the Sole Octotricopeptide Repeat Protein in Arabidopsis, Is Required for Chloroplast 16S rRNA Maturation
Laura Kleinknecht,Fei Wang,Roland Stübe,Katrin Philippar,Jörg Nickelsen,Alexandra-Viola Bohne +5 more
TL;DR: The characterization of the only OPR protein in Arabidopsis thaliana, RAP, revealed that RAP has an intrinsic and specific RNA binding capacity, and the RAP binding site was mapped to the 5′ region of the 16S rRNA precursor.
Journal ArticleDOI
Chloroplast RNA-binding and pentatricopeptide repeat proteins
TL;DR: This study focuses on two RNA-binding proteins: cpRNP (chloroplast ribonucleoprotein) and PPR (pentatricopeptide repeat) protein, suggested to be major contributors to chloroplast RNA metabolism.
Journal ArticleDOI
Molecular cloning of three malic acid related genes MdPEPC, MdVHA-A, MdcyME and their expression analysis in apple fruits
TL;DR: Real-time quantitative PCR discovered that the expression levels of three genes varied with development stages, and that their expression patterns differed between low acid (LA) and high acid (HA) genotypes.
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