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Output format



DESCRIPTION

The prediction output for each FASTA entry (each peptide) consists of

  • Pos
  • Peptide length
  • Peptide sequence
  • HLA allele
  • Prediction score (called 1-log50K(aff))
  • Affinity as IC50 value in nM (only for white-listed alleles)
  • %Random - %Rank of prediction score to a set of 1000.000 random natural 9mer peptides
  • Binding level (SB: strong binder, WB: weak binder)
  • Estimated accuracy of predictions for the given HLA allele



  • EXAMPLE OUTPUT

    
    
    
    # HLArestrictor with NetMHCpan version 2.4
    # HLA types used:  HLA-A01:01,  HLA-A02:01,  HLA-A03:01,  HLA-A24:02
    # Peptide lengths:  9,  10
    # Sort-method: OR.  Sort-mode: HLA-oriented
    # %rank threshold for strong binding peptides: 0.5%rank
    # %rank threshold for weak binding peptides: 2.0%rank
    # Affinity threshold for strong binding peptides: 50.0nM
    # Affinity threshold for weak binding peptides: 500.0nM
    # Number of predictions per peptide: Not specified
    # Non-binders shown up to a prediction score of 2.0*(weak binding threshold)
    
    
    Results for Peptide pep1: HGLMNPDATVRKNVL 
    --------------------------------------------------------------------------
    Pos	Length	Peptide		HLA	1-log50k(aff)	Affinity(nM)	%Rank		Label		Estimated prediction accuracy
    
    
    2	9	GLMNPDATV	HLA-A02:01	0.718		21		0.8		Weak binder	0.853
    
    3	10	LMNPDATVRK	HLA-A03:01	0.588		86		0.4		Strong binder	0.853
    2	10	GLMNPDATVR	HLA-A03:01	0.326		1464		3.0		Non-binder	0.853
    3	9	LMNPDATVR	HLA-A03:01	0.3		1947		3.0		Non-binder	0.853
    
    
    
    Results for Peptide pep2: DAVLQRDLVMEPGTAQY 
    --------------------------------------------------------------------------
    Pos	Length	Peptide		HLA	1-log50k(aff)	Affinity(nM)	%Rank		Label		Estimated prediction accuracy
    
    
    9	9	VMEPGTAQY	HLA-A01:01	0.455		364		0.8		Weak binder	0.853
    8	10	LVMEPGTAQY	HLA-A01:01	0.376		857		1.0		Weak binder	0.853
    
    8	10	LVMEPGTAQY	HLA-A03:01	0.328		1445		3.0		Non-binder	0.853
    9	9	VMEPGTAQY	HLA-A03:01	0.325		1491		3.0		Non-binder	0.853
    



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