Additional file 2.

Predictive performance in terms of the AUC on the IEDB El-Manzalawy benchmark. The methods included are NN-W-P1 (the NN-based method including data redundancy step-size rescaling and P1-PSSM encoding), NN-W (the NN-based method including data redundancy step-size rescaling), CTD, LA, and 5-spectrum. The performance values for the latter three methods are taken from the El-Manzalawy publication [25]. The benchmark data sets are UPDS: Unique peptides from the IEDB database, SRDS1: Sequence similarity reduced UPDS data excluding peptides sharing 9 mer subsequences, and SRDS2: Sequence similarity reduced SRDS1 data ensuring maximum more than 80% sequence similarity between pairs of peptides. For each allele, the best performing of all methods is underlined.

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Nielsen and Lund BMC Bioinformatics 2009 10:296   doi:10.1186/1471-2105-10-296