Table 2

Details of the benchmark calculation covering the 14 HLA-DR alleles.

AUC


Allele

SMM

Gibbs

TEPITOPE

SVRMHC

MHCpred

ARB

SMM -PRF

NetMHCII

N


1*0101

0.702

0.676

0.647

0.623

0.565

0.666

0.716

0.716

1203

1*0301

0.779

0.722

0.734

0.799

0.770

0.765

474

1*0401

0.741

0.759

0.754

0.739

0.606

0.737

0.756

0.758

457

1*0404

0.798

0.743

0.829

0.788

0.808

0.785

168

1*0405

0.727

0.724

0.790

0.701

0.724

0.733

0.735

171

1*0701

0.768

0.695

0.768

0.647

0.749

0.774

0.787

310

1*0802

0.724

0.721

0.769

0.803

0.740

0.756

174

1*0901

0.726

0.734

0.711

0.759

0.775

117

1*1101

0.715

0.715

0.710

0.727

0.720

0.734

359

1*1302

0.810

0.716

0.720

0.917

0.819

0.818

179

1*1501

0.715

0.672

0.726

0.730

0.792

0.733

0.736

365

3*0101

0.620

0.512

0.717

0.771

0.815

102

4*0101

0.730

0.742

0.800

0.729

0.736

181

5*0101

0.664

0.618

0.653

0.649

0.677

0.655

0.664

343


The predictive performance is shown in terms of the area under the ROC curve (AUC) for the SMM-align, Gibbs sampler [4], TEPITOPE [3], SVRMHC [7], MHCpred [15], and ARB methods, respectively. The SMM-PRF method refers to the extended SMM align method including penalties for long peptides and short amino terminal peptide flanking residues, and the NetMHCII method refers to the final extended SMM align method including direct encoding of peptide flanking residues and penalties for longer peptides and short amino terminal peptide flanking residues. The first column gives the allele names as 1*0101 for DRB1*0101 etc The last column gives the number of peptide data included for each allele. For each allele, the performance of the SMM-align, Gibbs sampler, and NetMHCII methods was estimated using five-fold cross-validation as described in the text. The details of the benchmark calculation as measured in terms of the Pearson's and Spearman's rank correlation are shown in Supplementary materials table 1 [see Additional file 1].

Nielsen et al. BMC Bioinformatics 2007 8:238   doi:10.1186/1471-2105-8-238

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