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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. 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

    
    
    NetMHC version 2.1. Prediction using Neural Networks. Allele A0101.
    High binder threshold  50.00. Weak binder threshold 500.00.
    
    --------------------------------------------------
     pos    peptide 1-log50k(aff) affinity(nM) Bind Level     Identity
    --------------------------------------------------
      54  ISERILSTY        0.6109           67         WB   gi|3333147
      66  STEPVPLQL        0.1893         6447              gi|3333147
      92  GTQQSQGVE        0.0964        17618              gi|3333147
      65  RSTEPVPLQ        0.0923        18427              gi|3333147
    ...
    --------------------------------------------------
    
    Number of high binders 0. Number of weak binders 1. Number of peptides 115
    
    --------------------------------------------------
    



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