Output format

EXAMPLE OUTPUT

For the following FASTA input example:

>P9WNK5
MAEMKTDAATLAQEAGNFERISGDLKTQIDQVESTAGSLQGQWRGAAGTAAQAAVVRFQEAANKQKQELDEISTNIRQAGVQYSRADEEQQQALSSQMGF

With parameters:

Peptide length: 15
Allele: DQA10301-DQB10302
Sort by prediction score: On

NetMHCIIpan-4.2 will return the following output (showing the top 10 predicted peptides):



# NetMHCIIpan version 4.2

# Input is in FASTA format

# Peptide length 15

# Prediction Mode: EL

# Threshold for Strong binding peptides (%Rank)	1%
# Threshold for Weak binding peptides (%Rank)	5%

# DQA10301-DQB10302 : Distance to training data 0.0000 (using nearest neighbor HLA-DQA10301-DQB10302)

# Allele: DQA10301-DQB10302
--------------------------------------------------------------------------------------------------------------------------------------------
 Pos                     MHC              Peptide   Of        Core  Core_Rel        Identity      Score_EL %Rank_EL Exp_Bind  BindLevel
--------------------------------------------------------------------------------------------------------------------------------------------
   3       DQA10301-DQB10302      EMKTDAATLAQEAGN    4   DAATLAQEA     0.590          P9WNK5      0.467401     0.23       NA   <=SB
  78       DQA10301-DQB10302      QAGVQYSRADEEQQQ    3   VQYSRADEE     0.900          P9WNK5      0.418179     0.35       NA   <=SB
   4       DQA10301-DQB10302      MKTDAATLAQEAGNF    3   DAATLAQEA     0.770          P9WNK5      0.406498     0.38       NA   <=SB
   2       DQA10301-DQB10302      AEMKTDAATLAQEAG    5   DAATLAQEA     0.530          P9WNK5      0.381155     0.47       NA   <=SB
  77       DQA10301-DQB10302      RQAGVQYSRADEEQQ    4   VQYSRADEE     0.890          P9WNK5      0.348975     0.64       NA   <=SB
   5       DQA10301-DQB10302      KTDAATLAQEAGNFE    2   DAATLAQEA     0.790          P9WNK5      0.325364     0.79       NA   <=SB
  79       DQA10301-DQB10302      AGVQYSRADEEQQQA    2   VQYSRADEE     0.740          P9WNK5      0.295187     1.03       NA   <=WB
   1       DQA10301-DQB10302      MAEMKTDAATLAQEA    6   DAATLAQEA     0.420          P9WNK5      0.260940     1.41       NA   <=WB
  76       DQA10301-DQB10302      IRQAGVQYSRADEEQ    5   VQYSRADEE     0.960          P9WNK5      0.250306     1.54       NA   <=WB
  80       DQA10301-DQB10302      GVQYSRADEEQQQAL    1   VQYSRADEE     0.600          P9WNK5      0.160670     3.56       NA   <=WB

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

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.