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Output format


Classical format

For each input sequence the following is shown (see the example below):
  • FASTA-like header line: a line showing the sequence name and length.

  • Prediction lines: one line per residue and kinase, with six columns in the form:

    1. Sequence - the sequence name;
    2. # - the position of the residue in the sequence;
    3. x - the residue in one-letter code;
    4. Context - the sequence context of the residue, shown as a 9-residue subsequence centered on the residue;
    5. Score - the prediction score (a value in the range [0.000-1.000]; the scores above 0.500 indicate positive predictions);
    6. Kinase - the active kinase or the string "unsp" for non-specific prediction (as in NetPhos 2.0);
    7. Answer - the string "YES" for positive predictions, else a dot.

  • Sequence - the input sequence as processed by NetPhos, with an overview of the positions of the predicted sites.

  • Graphics - a plot of scores illustrating the predictions. NOTE: for each residue only the highest score is shown.


GFF

The output in GFF ( GFF version 2) provides essentially the same information as the classical format described above. The only differences, apart from the syntax, are as follows:
  • the sequence context of the residues is not provided
  • the positive predictions are indicated by "Y" (not "YES")
This option has been provided for the benefit of the users who have access to software parsing GFF.


Example

The NetPhos 3.1 output for the UniProtKB entry P53_HUMAN (P04637). The predictions are for tyrosine only, showing only the highest scoring prediction for each residue and skipping all the predictions with scores lower than 0.250.


Classical format

>P53_HUMAN	393 amino acids
#
# netphos-3.1b prediction results
#
# Sequence		   # x   Context     Score   Kinase    Answer
# -------------------------------------------------------------------
# P53_HUMAN               18 T   LSQETFSDL   0.582   CKI        YES
# P53_HUMAN               55 T   EQWFTEDPG   0.598   CKII       YES
# P53_HUMAN               81 T   PAAPTPAAP   0.704   unsp       YES
# P53_HUMAN              102 T   PSQKTYQGS   0.472   cdc2        . 
# P53_HUMAN              118 T   LHSGTAKSV   0.654   PKC        YES
# P53_HUMAN              123 T   AKSVTCTYS   0.455   GSK3        . 
# P53_HUMAN              125 T   SVTCTYSPA   0.684   PKC        YES
# P53_HUMAN              140 T   QLAKTCPVQ   0.479   cdc2        . 
# P53_HUMAN              150 T   WVDSTPPPG   0.599   unsp       YES
# P53_HUMAN              155 T   PPPGTRVRA   0.829   unsp       YES
# P53_HUMAN              170 T   SQHMTEVVR   0.482   unsp        . 
# P53_HUMAN              211 T   DDRNTFRHS   0.951   unsp       YES
# P53_HUMAN              230 T   GSDCTTIHY   0.438   GSK3        . 
# P53_HUMAN              231 T   SDCTTIHYN   0.454   GSK3        . 
# P53_HUMAN              253 T   RPILTIITL   0.467   CaM-II      . 
# P53_HUMAN              256 T   LTIITLEDS   0.492   cdc2        . 
# P53_HUMAN              284 T   RDRRTEEEN   0.865   unsp       YES
# P53_HUMAN              304 T   PPGSTKRAL   0.939   unsp       YES
# P53_HUMAN              312 T   LPNNTSSSP   0.459   CaM-II      . 
# P53_HUMAN              329 T   GEYFTLQIR   0.443   GSK3        . 
# P53_HUMAN              377 T   KGQSTSRHK   0.932   unsp       YES
# P53_HUMAN              387 T   LMFKTEGPD   0.440   GSK3        . 
#
    MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDI   #     50
    EQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQ   #    100
    KTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDST   #    150
    PPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGN   #    200
    LRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRP   #    250
    ILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP   #    300
    PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALEL   #    350
    KDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD          #    400
%1  .................T................................   #     50
%1  ....T.........................T...................   #    100
%1  .................T......T........................T   #    150
%1  ....T.............................................   #    200
%1  ..........T.......................................   #    250
%1  .................................T................   #    300
%1  ...T..............................................   #    350
%1  ..........................T................


GFF

The corresponding output in GFF (the graph is not shown again):

##gff-version 2
##source-version netphos-3.1b
##date 2016-07-12
##Type Protein P53_HUMAN
##Protein P53_HUMAN
##MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP
##DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK
##SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHE
##RCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS
##SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP
##PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPG
##GSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD                           
##end-Protein
# seqname            source        feature      start   end   score  N/A   ?
# ---------------------------------------------------------------------------
P53_HUMAN            netphos-3.1b  phos-CKI        18    18   0.582  . .  YES
P53_HUMAN            netphos-3.1b  phos-CKII       55    55   0.598  . .  YES
P53_HUMAN            netphos-3.1b  phos-unsp       81    81   0.704  . .  YES
P53_HUMAN            netphos-3.1b  phos-cdc2      102   102   0.472  . .   . 
P53_HUMAN            netphos-3.1b  phos-PKC       118   118   0.654  . .  YES
P53_HUMAN            netphos-3.1b  phos-GSK3      123   123   0.455  . .   . 
P53_HUMAN            netphos-3.1b  phos-PKC       125   125   0.684  . .  YES
P53_HUMAN            netphos-3.1b  phos-cdc2      140   140   0.479  . .   . 
P53_HUMAN            netphos-3.1b  phos-unsp      150   150   0.599  . .  YES
P53_HUMAN            netphos-3.1b  phos-unsp      155   155   0.829  . .  YES
P53_HUMAN            netphos-3.1b  phos-unsp      170   170   0.482  . .   . 
P53_HUMAN            netphos-3.1b  phos-unsp      211   211   0.951  . .  YES
P53_HUMAN            netphos-3.1b  phos-GSK3      230   230   0.438  . .   . 
P53_HUMAN            netphos-3.1b  phos-GSK3      231   231   0.454  . .   . 
P53_HUMAN            netphos-3.1b  phos-CaM-II    253   253   0.467  . .   . 
P53_HUMAN            netphos-3.1b  phos-cdc2      256   256   0.492  . .   . 
P53_HUMAN            netphos-3.1b  phos-unsp      284   284   0.865  . .  YES
P53_HUMAN            netphos-3.1b  phos-unsp      304   304   0.939  . .  YES
P53_HUMAN            netphos-3.1b  phos-CaM-II    312   312   0.459  . .   . 
P53_HUMAN            netphos-3.1b  phos-GSK3      329   329   0.443  . .   . 
P53_HUMAN            netphos-3.1b  phos-unsp      377   377   0.932  . .  YES
P53_HUMAN            netphos-3.1b  phos-GSK3      387   387   0.440  . .   . 



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