Output format

For each input sequence the server predicts the possibility of non-classical or leaderless secretion.

For each input sequence three scores are generated by SecretomeP server as shown below. The first score is the neural network output score. This score is the score presented in the reference paper. The second number represents the odds that the sequence in fact is secreted. The third score is an estimated posterior probability that the sequence is secreted. It is calculated be weighing the odds by a prior probability of 0.2%, and should thus not be confused with the true probability as the prior probability in your data set may be entirely different.

Even though SecretomeP is trained to predict non-classical or leaderless secretion, it usually gives high score to proteins entering the classical secretory pathway (through the ER-Golgi apparatus). Therefore, for the proteins in which the presence of a signal peptide is predicted by SignalP-2.0 a warning is added to the output.

# Name         NN-score  Odds   Weighted   Warning
#                               by prior
# ============================================================================
FGF1_HUMAN      0.847   4.267     0.009    -
FGF4_HUMAN      0.945   6.804     0.014    signal peptide predicted by SignalP
ATRX_HUMAN      0.093   0.205     0.000    -

In the example above the first protein, known to enter the non-classical secretory pathway, FGF1_HUMAN, is correctly predicted as secretory. The second classical secreted protein, FGF4_HUMAN, is correctly predicted as secretory, but a warning that a signal peptide is predicted is reported. The third protein, ATRX_HUMAN, a known nuclear protein, receives a low score, thus is correctly classified.