Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction

BMC Bioinformatics

Table 3 Representative alleles

Supertype	NetCTL	EpiJen	MAPPP	MHC-pathway	WAPP
A1	HLA-A*0101	HLA-A*0101	HLA-A1	HLA-A*0101	HLA-A*01
A2	HLA-A*0201	HLA-A*0201	HLA-A*0201	HLA-A*0201	HLA-A*0201
A3	HLA-A*0301	HLA-A*0301	HLA-A3	HLA-A*0301	HLA-A*03
A24	HLA-A*2402	HLA-A*24	HLA-A24	HLA-A*2402	N/A
A26	HLA-A*2601	N/A	N/A*	HLA-A*2601	N/A
B7	HLA-B*0702	HLA-B*07	HLA-B7	HLA-B*0702	N/A
B8	HLA-B*0801	N/A	HLA-B8	HLA-B*0801	N/A
B27	HLA-B*2705	HLA-B*27	HLA-B*2705	HLA-B*2705	HLA-B*2705
B39	HLA-B*3901	N/A	HLA-B*3901	N/A	N/A
B44	HLA-B*4001	HLA-B*40	HLA-B40	HLA-B*4002	N/A
B58	HLA-B*5801	N/A	HLA-B*5801	HLA-B*5801	N/A
B62	HLA-B*1501	N/A	HLA-B62	HLA-B*1501	N/A
# epitope-protein pairs	216	188	214	215	131

The table shows which alleles are used for representing the supertypes in the HIV and HIV^EpiJen datasets. The first column gives the HLA supertype, the next five columns give the alleles used a supertype representatives for each of the five prediction method NetCTL-1.2, EpiJen, MAPPP, MHC-pathway, and WAPP, respectively. The lower row (N) gives the total number of epitope-protein pairs in the HIV dataset covered by each of the five prediction methods. *A MHC type termed HLA-A26 was listed, but did not produce any results.

ISSN: 1471-2105