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Table 2 Methods for analyzing steps in the antigen-processing pathway and for HLA typing

From: Immunoinformatics and epitope prediction in the age of genomic medicine

Predictor/tool Key method Reference
HLA class I binding
 Allele-specific
  SYFPEITHI PSSM [14]
  RANKPEP PSSM [27]
  BIMAS PSSM [28]
  SVMHC SVM [7]
  netMHC ANN [29]
 Pan-specific
  MULTIPRED HMM/ANN [39]
  netMHCpan ANN [40]
  PickPocket PSSM [41]
  TEPITOPEpan PSSM [42]
  ADT Threading [43]
  UniTope SVM [44]
  KISS SVM [45]
HLA class II binding
 Allele-specific
  SYFPEITHI PSSM [14]
  netMHCII/SM-align PSSM/ANN [48, 49]
  ProPred PSSM [50]
  RANKPED PSSM [27]
  TEPITOPE PSSM [51]
  SVRMHC SVM [8]
  MHC2MIL Multi-instance learning [52]
  MHC2pred SVM
 Pan-specific
  MULTIPRED HMM/ANN [39]
  MHCIIMulti Multi-instance learning [55]
  TEPITOPEpan PSSM [42]
  netMHCIIpan ANN [56, 90]
 Consensus methods
  CONSENSUS [57]
  netMHCcon [56]
 Binding stability
  netMHCstab ANN [47]
Proteasomal cleavage
in vitro
  netChop 20S ANN [60]
  PCM PSSM [61]
  FragPredict PSSM [62]
  Pcleavage SVM [63]
  PAProC ANN [64]
in vivo
  netChop Cterm ANN [60]
  ProteaSMM PSSM [65]
TAP transport
 PredTAP HMM/ANN [39]
 SVMTAP SVM [61]
Integrated processing
 EpiJen [70]
 WAPP [61]
 NetCTL [71]
 NetCTLpan [72]
T-cell reactivity
 POPI SVM [74]
 POPISK SVM [75]
B-cell epitope prediction
 Continuous
  COBEpro SVM [78]
  BCPRed SVM [79]
  FBCPred SVM [79]
 Discontinuous
  EPMeta SVM [82]
  Discotope 2.0 Linear regression [83]
NGS-based HLA typing
 ATHLATES Contig assembly [25]
 seq2HLA Greedy algorithm [26]
 OptiType Integer linear programming [19]
 Polysolver Bayesian classification [20]
  1. Abbreviations: ANN artificial neural network, HLA human leukocyte antigen, HMM hidden Markov model, NGS next-generation sequencing, PSSM position-specific scoring matrix, SVM support vector machine, TAP transporter associated with antigen processing