NetOGlyc 3.1 Output format

Output format

DESCRIPTION

For each input sequence the following is shown (see the example below):

Header line, quoting the name and length of the sequence.
Sequence, in one-letter code, as it was interpreted by the server.
Annotation overview, showing the predictions residue by residue, as follows:

. (dot) neutral place-holder

_ (underscore) predicted signal peptide

S,T predicted O-glycosylation sites
Prediction score table, quoting the scores for each S and T residue in the sequence.
The G-score is the score from the best general predictor; the I-score is the score from the best isolated site predictor.
If the G-score is >0.5 the residue is predicted as glycosylated; the higher the score the more confident the prediction.
For threonines an additional score is used: if the G-score is <0.5 but the I-score >0.5 and there are no predicted neighbouring sites (distance <10 residues) the residue is also predicted as glycosylated.
If a residue in a predicted signal peptide is predicted as glycosylated there is a warning in the comment field.
Graphs, in GIF and PostScript, illustrating the predictions.
For each S and T the prediction score is plotted against the position in the sequence.

The example below shows the output for rhamnogalacturonan acetylesterase precursor (EC 3.1.1.-), taken from the Swiss-Prot entry RHA1_ASPAC. The signal peptide prediction is consistent with the database annotation. Two O-glycosylation sites are predicted, both threonine. One (pos. 3) is within the signal peptide and should be ignored.

If the signal peptide check is enabled and no signal peptide is predicted a warning is printed at the top of the output for that sequence (not shown here).

EXAMPLE OUTPUT

Name: RHA1_ASPAC Length: 250 MKTAALAPLFFLPSALATTVYLAGDSTMAKNGGGSGTNGWGEYLASYLSATVVNDAVAGRSARSYTREGRFENIADVVTA GDYVIVEFGHNDGGSLSTDNGRTDCSGTGAEVCYSVYDGVNETILTFPAYLENAAKLFTAKGAKVILSSQTPNNPWETGT FVNSPTRFVEYAELAAEVAGVEYVDHWSYVDSIYETLGNATVNSYFPIDHTHTSPAGAEVVAEAFLKAVVCTGTSLKSVL TTTSFEGTCL __T______________............................................................... ................................................................................ ................................................................................ .......T.. Name S/T Pos G-score I-score Y/N Comment ---------------------------------------------------------------------------- RHA1_ASPAC T 3 0.519 0.056 T signal peptide? RHA1_ASPAC S 14 0.262 0.094 . - RHA1_ASPAC T 18 0.349 0.070 . - RHA1_ASPAC T 19 0.339 0.036 . - RHA1_ASPAC S 26 0.292 0.019 . - RHA1_ASPAC T 27 0.405 0.021 . - RHA1_ASPAC S 35 0.234 0.031 . - RHA1_ASPAC T 37 0.351 0.042 . - RHA1_ASPAC S 46 0.228 0.037 . - RHA1_ASPAC S 49 0.255 0.076 . - RHA1_ASPAC T 51 0.328 0.160 . - RHA1_ASPAC S 61 0.271 0.023 . - RHA1_ASPAC S 64 0.315 0.025 . - RHA1_ASPAC T 66 0.391 0.056 . - RHA1_ASPAC T 79 0.254 0.185 . - RHA1_ASPAC S 95 0.239 0.037 . - RHA1_ASPAC S 97 0.259 0.050 . - RHA1_ASPAC T 98 0.358 0.080 . - RHA1_ASPAC T 103 0.339 0.051 . - RHA1_ASPAC S 106 0.236 0.027 . - RHA1_ASPAC T 108 0.361 0.091 . - RHA1_ASPAC S 115 0.217 0.053 . - RHA1_ASPAC T 123 0.238 0.038 . - RHA1_ASPAC T 126 0.228 0.144 . - RHA1_ASPAC T 139 0.293 0.057 . - RHA1_ASPAC S 148 0.279 0.287 . - RHA1_ASPAC S 149 0.301 0.273 . - RHA1_ASPAC T 151 0.467 0.098 . - RHA1_ASPAC T 158 0.474 0.079 . - RHA1_ASPAC T 160 0.486 0.019 . - RHA1_ASPAC S 164 0.370 0.022 . - RHA1_ASPAC T 166 0.469 0.055 . - RHA1_ASPAC S 188 0.190 0.031 . - RHA1_ASPAC S 192 0.204 0.018 . - RHA1_ASPAC T 196 0.272 0.062 . - RHA1_ASPAC T 201 0.385 0.035 . - RHA1_ASPAC S 204 0.312 0.029 . - RHA1_ASPAC T 211 0.456 0.030 . - RHA1_ASPAC T 213 0.417 0.063 . - RHA1_ASPAC S 214 0.306 0.100 . - RHA1_ASPAC T 232 0.364 0.094 . - RHA1_ASPAC T 234 0.375 0.019 . - RHA1_ASPAC S 235 0.272 0.029 . - RHA1_ASPAC S 238 0.258 0.036 . - RHA1_ASPAC T 241 0.400 0.067 . - RHA1_ASPAC T 242 0.443 0.289 . - RHA1_ASPAC T 243 0.491 0.024 . - RHA1_ASPAC S 244 0.413 0.025 . - RHA1_ASPAC T 248 0.542 0.018 T - ----------------------------------------------------------------------------

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