Prediction of MHC class I binding peptides, using SVMHC

BMC Bioinformatics

Table 2 Performance of SVMHC for different HLA alleles, using MHCPEP- or SYFPEITHI-data.

MHC	Length	Size	Mc	Kernel
Predictions using MHCPEP
HLA-A1	9	28	0.95	lin
HLA-A*1101	9	40	0.74	poly
HLA-A11	9	46	0.75	rbf
HLA-A11	10	21	0.59	poly
HLA-A2	9	118	0.76	poly
HLA-A2	10	35	0.65	poly
HLA-A*2402	9	73	0.90	poly
HLA-A3	9	73	0.76	rbf
HLA-A*0201	9	184	0.73	rbf
HLA-A*0201	10	96	0.78	poly
HLA-A*3301	9	32	0.72	lin
HLA-A*0301	9	38	0.72	rbf
HLA-A*0301	10	32	0.77	lin
HLA-A31	9	39	0.79	poly
HLA-A*6801	9	42	0.84	poly
HLA-B7	9	32	0.95	lin
HLA-B8	9	26	0.77	poly
HLA-B*2705	9	41	0.93	lin
HLA-B*3501	9	67	0.93	lin
HLA-B*3501	10	34	0.96	poly
HLA-B35	9	23	0.71	lin
HLA-B*2703	9	22	0.90	lin
HLA-B*5301	9	41	0.95	lin
HLA-B27	9	34	0.91	rbf
HLA-B*2706	9	20	0.93	lin
HLA-B51	9	67	0.82	poly
HLA-B*5102	9	29	0.79	poly
HLA-B*0702	9	52	0.96	poly
HLA-B*5103	9	29	0.84	rbf
HLA-B*5401	9	42	0.98	lin
HLA-B*5101	9	35	0.89	lin
Predictions using SYFPEITHI
HLA-A*0201	9	113	0.78	rbf
HLA-A*0201	10	40	0.70	poly
HLA-A1	9	28	0.96	lin
HLA-A3	9	73	0.80	lin
HLA-B*8	8	14	0.89	lin
HLA-B*8	9	25	0.79	lin
HLA-B*2705	9	29	1.00	lin
HLA-B7	9	23	0.93	lin

The first column explains shows the HLA allele, the second the length of the binding peptides, the third the number of binders included in the training set, the fourth the performance as measured by the Matthews correlation coefficient. The final column shows what type of kernel was used in the Support Vector Machine.

ISSN: 1471-2105