Output format

EXAMPLE OUTPUT

For the following FASTA input example:

>sp|Q16655|MAR1_HUMAN Melanoma antigen recognized by T-cells 1 OS=Homo sapiens OX=9606 GN=MLANA PE=1 SV=1
MPREDAHFIYGYPKKGHGHSYTTAEEAAGIGILTVILGVLLLIGCWYCRRRNGYRALMDK
SLHVGTQCALTRRCPQEGFDHRDSKVsLQEKNCEPVVPNAPPAyEKLsAEQSPPPysP

With parameters:

Peptide length: 15
Allele: DRB1_0101
Sort by prediction score: On

NetMHCIIphosPan-1.0 will return the following output (showing the top predicted peptides):


# NetMHCIIphosPan version 1.0a

# Input is in FASTA format

# Peptide length 15

# Prediction Mode: EL

# Threshold for Strong binding peptides (%Rank)  1.00%
# Threshold for Weak binding peptides (%Rank)    5.00%

# DRB1_0101 : Distance to training data  0.000 (using nearest neighbor DRB1_0101)

# Allele: DRB1_0101
--------------------------------------------------------------------------------------------------------------------------------------------
 Pos               MHC              Peptide   Of        Core  Core_Rel Inverted        Identity      Score_EL %Rank_EL  Exp_Bind  BindLevel
--------------------------------------------------------------------------------------------------------------------------------------------
 101         DRB1_0101      PPAyEKLsAEQSPPP    3   yEKLsAEQS     1.000        0 sp_Q16655_MAR1_      0.866951     0.09        NA   <= SB
  85         DRB1_0101      KVsLQEKNCEPVVPN    3   LQEKNCEPV     0.900        0 sp_Q16655_MAR1_      0.034566    14.72        NA
  82         DRB1_0101      RDSKVsLQEKNCEPV    3   KVsLQEKNC     0.720        0 sp_Q16655_MAR1_      0.020288    19.72        NA
  76         DRB1_0101      QEGFDHRDSKVsLQE    3   FDHRDSKVs     0.960        0 sp_Q16655_MAR1_      0.019929    19.89        NA
  93         DRB1_0101      CEPVVPNAPPAyEKL    3   VVPNAPPAy     0.930        0 sp_Q16655_MAR1_      0.011383    25.98        NA
  83         DRB1_0101      DSKVsLQEKNCEPVV    3   VsLQEKNCE     0.100        0 sp_Q16655_MAR1_      0.006428    32.83        NA
  90         DRB1_0101      EKNCEPVVPNAPPAy    3   CEPVVPNAP     0.690        0 sp_Q16655_MAR1_      0.001225    54.80        NA
  97         DRB1_0101      VPNAPPAyEKLsAEQ    3   APPAyEKLs     0.310        0 sp_Q16655_MAR1_      0.000078    87.60        NA
--------------------------------------------------------------------------------------------------------------------------------------------
Number of strong binders: 1 Number of weak binders: 0
--------------------------------------------------------------------------------------------------------------------------------------------

DESCRIPTION

The prediction output for each molecule consists of the following columns:

Pos Residue number (starting from 0)

MHC MHC molecule name

Peptide Amino acid sequence

Of Starting position offset of the optimal binding core (starting from 0)

Core Binding core register

Core_Rel Reliability of the binding core, expressed as the fraction of networks in the ensemble selecting the optimal core

Inverted Whether the peptide binds inverted to the given MHC molecule (1: inverted, 0: forward)

Identity Annotation of the input sequence, if specified

Score_EL Eluted ligand prediction score

%Rank_EL Percentile rank of eluted ligand prediction score

Exp_bind If the input was given in PEPTIDE format with an annotated affinity value (mainly for benchmarking purposes).

Score_BA Predicted binding affinity in log-scale (printed only if binding affinity predictions were selected)

Affinity(nM) Predicted binding affinity in nanomolar IC50 (printed only if binding affinity predictions were selected)

%Rank_BA % Rank of predicted affinity compared to a set of 100.000 random natural peptides. This measure is not affected by inherent bias of certain molecules towards higher or lower mean predicted affinities (printed only if binding affinity predictions were selected)

BindLevel (SB: strong binder, WB: weak binder). The peptide will be identified as a strong binder if the % Rank is below the specified threshold for the strong binders. The peptide will be identified as a weak binder if the % Rank is above the threshold of the strong binders but below the specified threshold for the weak binders.