VIGOR extended to annotate genomes for additional 12 different viruses

Wang, Shiliang; Sundaram, Jaideep P.; Stockwell, Timothy B.

YFV and JEV are single-stranded, positive sense RNA viruses and belong to viral family Flaviviridae. The genome sizes of these viruses are 11 kb and only a single long polyprotein is encoded in these genomes. This long polyprotein will be co-and post-translationally processed into 10 to 11 mature peptides by host signal peptidases and a virus-encoded serine protease. The three mature peptides (C, PrM/M and E) from the N-terminus of the polyprotein are structural proteins, and the other seven or eight mature peptides from the C-terminus are non-structural proteins. One hundred seventy complete genomes of both YFV and JEV were tested by VIGOR, a total of 170 polyprotein genes were predicted by VIGOR because only a single gene is encoded in each genome (13, 14) . The start and stop codons of these genes were in complete agreement with GenBank annotations ( Table 1 ). The polyprotein of JEV is cleaved into 10 mature peptides (13) . Eleven mature peptides are encoded in YFV genome (14) . VIGOR was able to identify the mature peptide cleavage sites accurately and predicted 10 and 11 mature peptides in the genomes of these two viruses. Only a small number of genomes of these two viruses have their mature peptides annotated in GenBank. We compared the available limited data with VIGOR predictions. VIGOR mature peptide predictions agreed with GenBank records (data not shown). The conserved signature sequences for cleavage sites were also observed in VIGOR predictions.