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Pipeline publication

[…] b' Fisher Scientific Inc. (Waltham, MA, USA), and the primers specific for human EPS8 and GAPDH were synthesized by Sangon Biotech Co., Ltd (Shanghai, China)., To identify the potential T-cell epitopes for EPS8, the HLA-A*0201 allele was screened, covering a wide range of populations (). First, the protein sequence was screened for the best binding epitopes using the algorithms SYFPEITHI ( and Bioinformatics and Molecular Analysis Section (BIMAS; The cut-off score was adjusted to >20 for SYFPEITHI and T1/2>100 for BIMAS, and peptides matching these two criteria and which were shared by the two algorithms were selected. Second, the NetChop algorithm ( was used to predict whether the selected peptides in the first step would be cleaved at the C-terminus. Third, protein sequences were analyzed with five different algorithms for HLA-A*0201, including immune epitope database (IEDB;, NetMHC (, SVMHC (, EpiJen ( and Rankpep ( Peptides predicted by at least four algorithms were selected. The known HLA-A*0201-restricted carcinoembryonic antigen peptide-1 (CAP-1, YLSGANLNL) was used as a positive control peptide (), while the HBcAg-derived HLA-A*2402-restricted peptide HBc117e125 (EYLVSFGVW) was used as a negative control peptide (), and all peptides were synthesized using standard 9-fluorenylmethyl-oxycarbonyl chemistry by the Chinese Peptide Company (Hangzhou, China). They were of >95% purity as determined by reverse-phase chromatography and their ide' […]

Pipeline specifications

Software tools NetChop, NetMHC, SVMHC