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. High binding peptides have an IC50 value below 50 nM, and weak binding peptides an IC50 values below 500 nM. 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

    
NetMHCII version 2.2. 

Strong binder threshold  50.00. Weak binder threshold 500.00.

-----------------------------------------------------------------------------------------------
      Allele  pos          peptide       core 1-log50k(aff) affinity(nM) Bind Level  %Random     Identity
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HLA-DRB10301    0  ASQKRPSQRHGSKYL  SQKRPSQRH        0.0444      30932.9               50.00   seq2 optio
HLA-DRB10301    1  SQKRPSQRHGSKYLA  SQRHGSKYL        0.0456      30519.7               50.00   seq2 optio
HLA-DRB10301    2  QKRPSQRHGSKYLAT  SQRHGSKYL        0.0492      29375.3               50.00   seq2 optio
HLA-DRB10301    3  KRPSQRHGSKYLATA  SQRHGSKYL        0.0581      26676.2               50.00   seq2 optio
HLA-DRB10301    4  RPSQRHGSKYLATAS  SQRHGSKYL        0.0528      28231.7               50.00   seq2 optio
...
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Allele: HLA-DRB10301. Number of high binders 0. Number of weak binders 5. Number of peptides 138

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