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Output format

Description of the scores
Examples of standard output
Examples of short output


DESCRIPTION OF THE SCORES

The graphical output from SignalP (neural network) comprises three different scores, C, S and Y. Two additional scores are reported in the SignalP output, namely the S-mean and the D-score, but these are only reported as numerical values.

For each organism class in SignalP; Eukaryote, Gram-negative and Gram-positive, two different neural networks are used, one for predicting the actual signal peptide and one for predicting the position of the signal peptidase I (SPase I) cleavage site. The S-score for the signal peptide prediction is reported for every single amino acid position in the submitted sequence, with high scores indicating that the corresponding amino acid is part of a signal peptide, and low scores indicating that the amino acid is part of a mature protein.

The C-score is the ``cleavage site'' score. For each position in the submitted sequence, a C-score is reported, which should only be significantly high at the cleavage site. Confusion is often seen with the position numbering of the cleavage site. When a cleavage site position is referred to by a single number, the number indicates the first residue in the mature protein, meaning that a reported cleavage site between amino acid 26-27 corresponds to that the mature protein starts at (and include) position 27.

Y-max is a derivative of the C-score combined with the S-score resulting in a better cleavage site prediction than the raw C-score alone. This is due to the fact that multiple high-peaking C-scores can be found in one sequence, where only one is the true cleavage site. The cleavage site is assigned from the Y-score where the slope of the S-score is steep and a significant C-score is found.

The S-mean is the average of the S-score, ranging from the N-terminal amino acid to the amino acid assigned with the highest Y-max score, thus the S-mean score is calculated for the length of the predicted signal peptide. The S-mean score was in SignalP version 2.0 used as the criteria for discrimination of secretory and non-secretory proteins.

The D-score is introduced in SignalP version 3.0. In version 4.0 this score is implemented as a weighted average of the S-mean and the Y-max scores. The score shows superior discrimination performance of secretory and non-secretory proteins to that of the S-mean score which was used in SignalP version 1 and 2.

For non-secretory proteins all the scores represented in the SignalP output should ideally be very low.


EXAMPLES OF STANDARD OUTPUT

By default the server produces the following output for each input sequence:

Example 1: secretory protein - default output

The example below shows the output for thioredoxin domain containing protein 4 precursor (endoplasmic reticulum protein ERp44), taken from the
Swiss-Prot entry ERP44_HUMAN. The signal peptide prediction is consistent with the database annotation.

ERP44_HUMAN

SignalP result:


# Measure Position Value # max. C 30 0.427 # max. Y 30 0.586 # max. S 9 0.950 # mean S 1-29 0.821 # D 1-29 0.713 # ERP44_HUMAN SP= 'Yes' Cleavage site between pos. 29 and 30: VTT-EI D= 0.713 D-cutoff= 0.450 Networks= SignalP-noTM # data # gnuplot script Signal peptides: 1 # processed fasta entries # gff file of processed entries


Example 2: short output format

# SignalP-4.0 euk predictions
# name                     Cmax  pos  Ymax  pos  Smax  pos  Smean   D     ?  Dmaxcut    Networks-used
ERP44_HUMAN                0.427  30  0.586  30  0.950   9  0.821   0.713 Y  0.450      SignalP-noTM



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