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Output format



DESCRIPTION

The output provides common information for all the alleles:

  • What was the input format (FASTA or PEPTIDE)

  • Peptide length

  • Thresholds used to identify strong and weak binders


    The prediction output for each allele consists of 10 or 11 columns:

  • Residue number (starting from 0)

  • Allele name

  • Peptide sequence

  • Protein identifier

  • Start position of the binding core (starting from 0)

  • Binding core

  • Prediction score (called 1-log50K(aff))

  • Affinity as IC50 value in nM (only for white-listed alleles)

  • %Rank - % Rank of prediction score to a set of 200.000 random natural 9mer peptides

  • Expected binding affinity if the input was given in PEPTIDE format and provided peptides had expected binding affinity values.

  • Binding level (SB: strong binder, WB: weak binder). The peptide will be identified as a strong binder if the % Rank OR binding affinity (IC50) is below the specified threshold for the strong binders. The peptide will be identified as a weak binder if the % Rank OR binding affinity (IC50) is above the threshold of the strong binders but below the specified threshold for the weak binders.

    Fianlly, at the end of predictions for each allele, the numbers of total strong and weak binders are given.


  • EXAMPLE OUTPUT

    
    
    # NetMHCIIpan version 3.0
    
    # Input is in FASTA format
    
    # Peptide length 15
    
    # Threshold for Strong binding peptides (IC50)	50.000 nM
    # Threshold for Weak binding peptides (IC50)	500.000 nM
    
    # Threshold for Strong binding peptides (%Rank)	0.5%
    # Threshold for Weak binding peptides (%Rank)	2%
    
    
    
    
    # Allele: HLA-DPA10104-DPB10301
    -------------------------------------------------------------------------------------------------------------------------------------------
       pos                 Allele           peptide    Identity  Pos         Core 1-log50k(aff)  Affinity(nM)  %Rank   BindingLevel
    -------------------------------------------------------------------------------------------------------------------------------------------
         0  HLA-DPA10104-DPB10301   ASQKRPSQRHGSKYL        seq2    6    SQRHGSKYL         0.167       8228.18  50.00  
         1  HLA-DPA10104-DPB10301   SQKRPSQRHGSKYLA        seq2    5    SQRHGSKYL         0.194       6153.37  50.00  
         2  HLA-DPA10104-DPB10301   QKRPSQRHGSKYLAT        seq2    4    SQRHGSKYL         0.259       3021.00  50.00  
         3  HLA-DPA10104-DPB10301   KRPSQRHGSKYLATA        seq2    3    SQRHGSKYL         0.293       2094.80  50.00  
         4  HLA-DPA10104-DPB10301   RPSQRHGSKYLATAS        seq2    4    RHGSKYLAT         0.305       1850.86  50.00  
         5  HLA-DPA10104-DPB10301   PSQRHGSKYLATAST        seq2    3    RHGSKYLAT         0.313       1683.89  50.00  
         6  HLA-DPA10104-DPB10301   SQRHGSKYLATASTM        seq2    6    KYLATASTM         0.424        507.28  50.00  
         7  HLA-DPA10104-DPB10301   QRHGSKYLATASTMD        seq2    5    KYLATASTM         0.475        293.10  50.00  <=WB
         8  HLA-DPA10104-DPB10301   RHGSKYLATASTMDH        seq2    4    KYLATASTM         0.515        189.11  32.00  <=WB
         9  HLA-DPA10104-DPB10301   HGSKYLATASTMDHA        seq2    3    KYLATASTM         0.549        132.25  32.00  <=WB
        10  HLA-DPA10104-DPB10301   GSKYLATASTMDHAR        seq2    3    YLATASTMD         0.562        114.61  32.00  <=WB
        11  HLA-DPA10104-DPB10301   SKYLATASTMDHARH        seq2    2    YLATASTMD         0.553        125.65  32.00  <=WB
        12  HLA-DPA10104-DPB10301   KYLATASTMDHARHG        seq2    0    KYLATASTM         0.519        182.96  32.00  <=WB
        13  HLA-DPA10104-DPB10301   YLATASTMDHARHGF        seq2    0    YLATASTMD         0.349       1145.85  50.00  
        14  HLA-DPA10104-DPB10301   LATASTMDHARHGFL        seq2    0    LATASTMDH         0.288       2216.01  50.00  
        15  HLA-DPA10104-DPB10301   ATASTMDHARHGFLP        seq2    5    MDHARHGFL         0.258       3078.05  50.00  
        16  HLA-DPA10104-DPB10301   TASTMDHARHGFLPR        seq2    4    MDHARHGFL         0.301       1915.81  50.00  
        17  HLA-DPA10104-DPB10301   ASTMDHARHGFLPRH        seq2    3    MDHARHGFL         0.326       1475.42  50.00  
        18  HLA-DPA10104-DPB10301   STMDHARHGFLPRHR        seq2    4    HARHGFLPR         0.340       1266.81  50.00  
        19  HLA-DPA10104-DPB10301   TMDHARHGFLPRHRD        seq2    3    HARHGFLPR         0.333       1357.17  50.00  
        20  HLA-DPA10104-DPB10301   MDHARHGFLPRHRDT        seq2    2    HARHGFLPR         0.324       1497.74  50.00  
        21  HLA-DPA10104-DPB10301   DHARHGFLPRHRDTG        seq2    1    HARHGFLPR         0.285       2298.56  50.00  
        22  HLA-DPA10104-DPB10301   HARHGFLPRHRDTGI        seq2    2    RHGFLPRHR         0.288       2208.57  50.00  
        23  HLA-DPA10104-DPB10301   ARHGFLPRHRDTGIL        seq2    1    RHGFLPRHR         0.251       3309.79  50.00  
    
    
    
    



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