Name is the name of the submitted sequence, truncated if longer than 11
characters.
Length is the length (!) of the submitted sequence.
Score is the output score from the second step network. The prediction
cTP/no cTP is based solely on this score.
cTP tells whether or not this is predicted as a cTP-containing sequence;
"Y" means that the sequence is predicted to contain a cTP; "-" means
that is predicted not to contain a cTP.
CS-score is the MEME scoring matrix score for the suggested cleavage
site.
cTP-length is the predicted length of the presequence (Please
note that the prediction of the transit peptide length is carried out and
presented even if its presence is not predicted).
Shown only if "Detailed output" was chosen:
NN-score, Raw is the score for each residue from the first step
network.
NN-score, Deriv. is a numerical derivative of the network score. Used
for finding the amino acid stretch of 40 residues in which the cleavage site is
searched.
CS-score (cleavage site score) is the MEME scoring matrix score, defined
so that the predicted cleavage site is directly N-terminal of the highest
scoring residue.
Additional information
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 are
presented. The higher the score, the more certain is the network that this
sequence contains an N-terminal chloroplast transit peptide (cTP).
If "Detailed output" was 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, and
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).