Volume 7, Number 4—August 2001
THEME ISSUE
West Nile Virus
West Nile Virus
Rapid Determination of HLA B*07 Ligands from the West Nile Virus NY99 Genome
Table 1
Scoring overlapping peptides by the EpiMatrix motif HLA B*07 EpiMatrix analysis of West Nile virus protein NS-1
AA start | Peptide no. (B*07 rank) | Sequence | EBPa |
---|---|---|---|
1123 | WNB7 3119 | GMEIRPQRHD | 0.04 |
1124 | WNB7 2818 | MEIRPQRHDE | 0.08 |
1125 | WNB7 0591 | EIRPQRHDEK | 1.12 |
1126 | WNB7 2660 | IRPQRHDEKT | 0.10 |
1127 | WNB7 0019 | RPQRHDEKTL | 22.49 |
1128 | WNB7 2661 | PQRHDEKTLV | 0.10 |
aEBP = estimated binding potential, which is the value that EpiMatrix uses to describe the probability that the peptide will bind to B*07 in vitro and in vivo. In this example, six overlapping peptides in the region of the WNV sequence coding for the NS-1 protein (WNV genome AA 1123 to 1128) are shown. WNVB7 0019 received the best EpiMatrix score (22.49) and was therefore selected for in vitro studies.