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Output format

The output from NetPhos contains three parts for each sequence analyzed.

The first part shows the name and length of the sequence followed by the amino acid sequence. Then follows an assignment field describing the predicted category for each residue. If the residue is predicted NOT to be phosphorylated, either because the score is below the threshold or because the residue is not Ser, Thr, or Tyr, that position is marked by a dot ('.'). Residues having a prediction score above the threshold are indicated by 'S', 'T' or 'Y', respectively.

Below the assignment line, the number of predicted S/T/Y phosphorylation sites is shown.

The second part describes the predictions for each type of residue (Ser, Thr or Tyr).

  • Column 1:   sequence name
  • Column 2:   position of the residue being analyzed
  • Column 3:   sequence context (shown as a 9-residue sequence centered on the residue being analyzed)
  • Column 4:   output score (value in the range [0.000-1.000])
  • Column 5:   assigment (scores above the threshold of 0.500 are assigned as '*S*', '*T*', or '*Y*')

The third part is a graph illustrating the predictions (can be omitted if the 'Generate graphics' button has been un-checked).


In the example below, T-7, S-18, Y-19, and Y-23 are predicted as potential phosphorylation sites. S-18 has a score of 0.942 indicating a very likely phosphorylation site, whereas Y-19 has a score of only 0.502. The latter score is  just barely above the threshold  (0.500) and indicates that the confidence for this site being a true phosphorylation site is quite low.

In general the higher the score, the higher the confidence of the prediction and the higher the similarity to one or more of the phosphorylation sites used in training the method.

Name:  test1            Length: 26  <-- Sequence name, length
QWERRRTYELVISLIVESYEAHYEAH          <-- Submitted sequence
......T..........SY...Y...          <-- Assignments. S,T,Y indicates

                                        predicted phosphorylation sites
Ser: 1  Thr: 1  Tyr: 2              <-- No. of predicted S,T,Y phosph. sites
                Serine predictions

Name           Pos   Context    Score  Pred
test1           13   ELVISLIVE  0.017    .
test1           18   LIVESYEAH  0.942  *S*

                Threonine predictions

Name           Pos   Context    Score  Pred
test1            7   ERRRTYELV  0.921  *T*

                Tyrosine predictions

Name           Pos   Context    Score  Pred
test1            8   RRRTYELVI  0.056    .
test1           19   IVESYEAHY  0.502  *Y*
test1           23   YEAHYEAH-  0.885  *Y*


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