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Output format



DESCRIPTION

In the header of the out is indicated which prediction method and HLA allele were selected, as well as the corresponding two threshold values defining high binding peptides, and weak binding peptides. For Artificial neural network prediction high binding peptides have an IC50 value below 50 nM, and weak binding peptides an IC50 values below 500 nM. For weight matrix prediction high binding peptides have a prediction score greater than the 0.1% precentile score value of 1.000.000 random natural peptides, and weak binding peptides a score value above the 1% percentile score of 1.000.000 random natural peptides.

In the header is a link to an .xls file which contains the output in a tab seperated text file. For the format of this file see: Description of xls file.

For Artificial Neural network (ANN) prediction the output consists of 6 columns. For weight matrix predictions the output consists of 5 columns:

  • Residue number.
  • Peptide sequence (9mer)
  • Prediction score (called 1-log50K(aff) for ANN predictions)
  • Affinity as IC50 value in nM (only for ANN predictions)
  • Bind Level (WB for weak binder, SB for strong binder)
  • Sequence name

    The predictions for each protein are summarized with a line stating the number of high and weak binding peptides identified.


  • EXAMPLE OUTPUT

    Using this fasta input:

    >Sequencename
    SLYNTVATLISINTHISLANGHDAKAK

    choosing peptide length 9, and the two alleles HLA-A*0201 and HLA-B*5801 will generate the following outputs:

    HTML Output

    Monday March 31 2008 10:41
    
    NetMHC version 3.0. 9mer predictions using Artificial Neural Networks. Allele A0201. 
    Strong binder threshold  50 nM. Weak binder threshold score 500 nM
    
    Download output sheet
    
    ----------------------------------------------------------------------------------------------------
     pos    peptide      logscore affinity(nM) Bind Level    Protein Name  Allele
    ----------------------------------------------------------------------------------------------------
       0  SLYNTVATL         0.529          162         WB    Sequencename   A0201
       1  LYNTVATLI         0.069        23754               Sequencename   A0201
       2  YNTVATLIS         0.025        38065               Sequencename   A0201
       3  NTVATLISI         0.328         1431               Sequencename   A0201
       4  TVATLISIN         0.022        39218               Sequencename   A0201
       5  VATLISINT         0.050        29197               Sequencename   A0201
       6  ATLISINTH         0.014        43052               Sequencename   A0201
       7  TLISINTHI         0.651           43         SB    Sequencename   A0201
       8  LISINTHIS         0.062        25445               Sequencename   A0201
       9  ISINTHISL         0.161         8805               Sequencename   A0201
      10  SINTHISLA         0.344         1203               Sequencename   A0201
      11  INTHISLAN         0.006        46655               Sequencename   A0201
      12  NTHISLANG         0.014        43114               Sequencename   A0201
      13  THISLANGH         0.002        48981               Sequencename   A0201
      14  HISLANGHD         0.005        47346               Sequencename   A0201
      15  ISLANGHDA         0.039        32840               Sequencename   A0201
      16  SLANGHDAK         0.039        32797               Sequencename   A0201
      17  LANGHDAKA         0.082        20602               Sequencename   A0201
      18  ANGHDAKAK         0.001        49359               Sequencename   A0201
    --------------------------------------------------------------------------------------------------
    
    NetMHC version 3.0. 9mer predictions using Artificial Neural Networks. Allele B5801. 
    Strong binder threshold  50 nM. Weak binder threshold score 500 nM
    
    Download output sheet
    
    ----------------------------------------------------------------------------------------------------
     pos    peptide      logscore affinity(nM) Bind Level    Protein Name  Allele
    ----------------------------------------------------------------------------------------------------
       0  SLYNTVATL         0.071        23245               Sequencename   B5801
       1  LYNTVATLI         0.052        28467               Sequencename   B5801
       2  YNTVATLIS         0.039        32889               Sequencename   B5801
       3  NTVATLISI         0.072        22920               Sequencename   B5801
       4  TVATLISIN         0.020        40058               Sequencename   B5801
       5  VATLISINT         0.037        33503               Sequencename   B5801
       6  ATLISINTH         0.046        30393               Sequencename   B5801
       7  TLISINTHI         0.145        10428               Sequencename   B5801
       8  LISINTHIS         0.028        36879               Sequencename   B5801
       9  ISINTHISL         0.488          255         WB    Sequencename   B5801
      10  SINTHISLA         0.020        40293               Sequencename   B5801
      11  INTHISLAN         0.024        38758               Sequencename   B5801
      12  NTHISLANG         0.018        41116               Sequencename   B5801
      13  THISLANGH         0.021        40026               Sequencename   B5801
      14  HISLANGHD         0.020        40200               Sequencename   B5801
      15  ISLANGHDA         0.062        25526               Sequencename   B5801
      16  SLANGHDAK         0.017        41400               Sequencename   B5801
      17  LANGHDAKA         0.068        23994               Sequencename   B5801
      18  ANGHDAKAK         0.013        43595               Sequencename   B5801
    --------------------------------------------------------------------------------------------------
    
    

    Description of xls file

    This file always contains the predicted peptides in the order they appeared in the input file. The output data for each peptide will be displayed on a single line with predictions for each of the selected alleles in different columns.

    The above FASTA input will give the following output when opened in Microsoft Excel:
    Column 1: The name of the protein
    Column 2: The position of the peptide within the full sequence
    Column 3: The sequence of the subpeptide for which the prediction is made
    Column 4 to
    Column N: The predicted affinity of the peptide to the MHC expressed by each of the chosen alleles
    Column N+1: An arbitrary mean score over all alleles. Useful for sorting peptides that binds to more than one allele.




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