Output format

C-score (raw cleavage site score)

The output score from networks trained to recognize cleavage sites vs. other sequence positions. Trained to be:

high	at position +1 (immediately after the cleavage site)
low	at all other positions.

S-score (signal peptide score)

The output score from networks trained to recognize signal peptide vs. non-signal-peptide positions. Trained to be:

high	at all positions before the cleavage site
low	at 30 positions after the cleavage site and in the N-terminals of non-secretory proteins.

Y-score (combined cleavage site score)

The prediction of cleavage site location is optimized by observing where the C-score is high and the S-score changes from a high to a low value. The Y-score formalizes this by combining the height of the C-score with the slope of the S-score.

Specifically, the Y-score is a geometric average between the C-score and a smoothed derivative of the S-score (i.e., the difference between the mean S-score over d positions before and d positions after the current position, where d varies with the chosen network ensemble).

All three scores are averages of five networks trained on different partitions of the data.

For each sequence, SignalP will report the maximal C-, S-, and Y-scores, and the mean S-score between the N-terminal and the predicted cleavage site. These values are used to distinguish between signal peptides and non-signal peptides. If the your sequence is predicted to have a signal peptide, the cleavage site is predicted to be immediately before the position with the maximal Y-score.

Graphics

For a typical signal peptide, the C- and Y-scores will be high at position +1, while the S-score will be high before the cleavage site and low thereafter:

In the following example, the true cleavage site would be incorrectly predicted when relying on the maximal value of the C-score alone, but SignalP is able to predict it correctly by using the combined Y-score (the true cleavage site is marked with an arrow):

For a typical non-secretory protein, all three scores are very low throughout the sequence:

In the following example, there are C-score and S-score peaks above the cutoff values, but SignalP is still able to classify it correctly as a non-secretory protein by using the Y-score or the mean value of the S-score (the C-score peak occurs far away from the S-score decline, and the region of high S-score is too short):

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