Format of output


DESCRIPTION

The output provides common information for all the alleles:

  • Which method was chosen to get the predictions
  • What was the input format (FASTA or PEPTIDE)
  • Peptide length(s)
  • Thresholds used to identify strong and weak binders

    For each allele the allele name is given and if NetMHCcons method was chosen, it is specified which method or combination of methods was used to get predictions for that allele.


    The prediction output for each allele consists of 8 columns:

  • Residue number
  • Allele name
  • Peptide sequence
  • Protein identifier
  • 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
  • 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

    

# Method: NetMHCcons

# Input is in FASTA format

# Peptide length 9

# 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-A01:01

# NetMHCcons = NetMHC+NetMHCpan

---------------------------------------------------------------------------------------
   pos       Allele         peptide         Identity 1-log50k(aff) Affinity(nM)  %Rank  BindingLevel
---------------------------------------------------------------------------------------
     0  HLA-A*01:01       ASTPGHTII             seq1         0.092     18478.42  15.00 
     1  HLA-A*01:01       STPGHTIIY             seq1         0.358      1044.93   0.80 <=WB
     2  HLA-A*01:01       TPGHTIIYE             seq1         0.038     32965.50  50.00 
     3  HLA-A*01:01       PGHTIIYEA             seq1         0.044     30893.41  50.00 
     4  HLA-A*01:01       GHTIIYEAV             seq1         0.057     27131.77  50.00 
     5  HLA-A*01:01       HTIIYEAVC             seq1         0.062     25564.30  32.00 
     6  HLA-A*01:01       TIIYEAVCL             seq1         0.057     27131.77  50.00 
     7  HLA-A*01:01       IIYEAVCLH             seq1         0.069     23571.74  32.00 
     8  HLA-A*01:01       IYEAVCLHN             seq1         0.046     30396.07  50.00 
     9  HLA-A*01:01       YEAVCLHND             seq1         0.037     33686.63  50.00 
    10  HLA-A*01:01       EAVCLHNDR             seq1         0.046     30232.07  50.00 
    11  HLA-A*01:01       AVCLHNDRT             seq1         0.050     29266.51  50.00 
    12  HLA-A*01:01       VCLHNDRTT             seq1         0.036     34053.09  50.00 
    13  HLA-A*01:01       CLHNDRTTI             seq1         0.061     25842.40  32.00 
    14  HLA-A*01:01       LHNDRTTIP             seq1         0.039     32787.64  50.00 
----------------------------------------------------------------------------------------
Number of strong binders: 0 Number of weak binders: 1
----------------------------------------------------------------------------------------