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Output format

On the result page, for each query sequence the name, the length, and the neural network output score on which the cTP/non-cTP assignment is based will be presented. The higher the score, the more certain is the network that this sequence contains an N-terminal chloroplast transit peptide (cTP). A potential cTP length will also be presented, along with the corresponding cleavage site score. Please note that the prediction of the transit peptide length is carried out even if its presence is not predicted. The purpose is to provide maximal information in borderline cases.

If "Detailed output" is chosen, the neural network score for each residue will also be presented. The higher this score, the more certain is the network that this residue is part of a cTP. A derivative of the network score is also presented. This score is used for finding the area in which the cleavage site is searched for - namely among the 40 residues surrounding the residue with the highest derivative score. Finally, the cleavage site score (CS-score) is presented for each residue. This score is calculated from a scoring matrix derived from an automatic motif finding algorithm called MEME. The cleavage site score is defined so that the predicted cleavage site is directly N-terminal of the highest scoring residue within the 40 residues. Thus, there might exist one or several CS-score(s) that happen(s) to be greater than the score of the proposed cTP length, but since they are located outside of the 40 residues around the highest derivative score, the presented cTP length is still what ChloroP considers as the most likely presequence length (ie. corresponding to the most likely cleavage site).


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