ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites.
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Cites background or methods from "ChloroP, a neural network-based met..."
...The full-size sets were also tested on PSORT (Nakai & Kanehisa, 1992; Horton & Nakai, 1997) and MitoProt (Claros, 1995; Claros & Vincens, 1996) as well as on TargetP's predecessors SignalP (Nielsen et al., 1997) and ChloroP (Emanuelsson et al., 1999)....
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...tested contains no sequences that participated in the development of teolytic activity in the stroma (Emanuelsson et al., 1999)....
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...The TargetP predictor has neural networks in two layers (Figure 2), roughly in the same manner as for ChloroP (Emanuelsson et al., 1999), with the ®rst layer consisting of one network for each type of presequence (i....
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..., 1997) or cTPs (ChloroP) (Emanuelsson et al., 1999) in a protein sequence....
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...…network architecture and training The TargetP predictor has neural networks in two layers (Figure 2), roughly in the same manner as for ChloroP (Emanuelsson et al., 1999), with the ®rst layer consisting of one network for each type of presequence (i.e. three in the plant version and two in the…...
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3,235 citations
Cites background from "ChloroP, a neural network-based met..."
...A motif, VRAmAAV, has been detected around the cleavage site (m...
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1,303 citations
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Cites methods from "ChloroP, a neural network-based met..."
...There are methods (Nakai and Kanehisa 1992; Nielsen et al. 1997; Emanuelsson et al. 1999, 2000; Nakai 2000) based on the observation that sequences targeted to specific locations rely on the N-terminal sorting or signal sequences....
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References
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"ChloroP, a neural network-based met..." refers methods in this paper
...…what is annotated in SWISS-PROT ~negative values!, 5 are correctly predicted, and only 3 predicted to be longer ~positive values!. neurons~Minsky & Papert, 1968! and zero or one layer of hidden units, trained using error backpropagation~Rumelhart et al., 1986!, but with different error functions....
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15,313 citations
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"ChloroP, a neural network-based met..." refers background or methods in this paper
...The initial set was screened for thylakoid transfer domains using the signal peptide predictor SignalP~Nielsen et al., 1997!, and homology reduction was carried out using the Hobohm algorithm 2~Hobohm et al., 1992!....
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...~Nielsen et al., 1997!, and those that were assigned a cleavage site within65 residues from the SWISS-PROT annotated cleavage site were excluded, since they most likely represent bi-partite stroma-thylakoid targeting sequences....
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...In several neural network applications, this has been handled by monitoring test set performance during training and picking the network where performance on the test set was optimal~Qian & Sejnowski, 1988; Brunak et al., 1991; Nielsen et al., 1997!....
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5,191 citations