Table 1.

Attributes of and citations for the epitope prediction programs used

Program	Prediction method	Unique features	Source paper (number of citations1)	URL
ARB	Average relative binding matrices		[42] (59)	[43]
MHCPred	Partial least squares		[33] (46)	[44]
			[34] (30)
			[35] (30)
ProPred	Matrix-based	TEPITOPE matrices; requires key anchor residues	[45] (186)	[41]
			TEPITOPE: [30] (310)
RankPep	Position Specific		[23] (119)	[47]
	Scoring Matrices		[46] (102)
NetMHCII	Position Specific Scoring Matrices	Predicts epitopes of multiple lengths; uses SMM-align matrices	[37] (29)	[48]
SVRMHC	Support vector machine regression		[32] (16)	[49]
			[31] (23)
Vaxign	Position Specific Scoring Matrices		[40] (0)	[50]
NetMHCIIpan	Artificial Neural Networks	Predicts multiple-length epitope binding to every sequenced Class II allele	[11] (3)	[51]

¹ Citation numbers are from Google Scholar