VIGOR extended to annotate genomes for additional 12 different viruses

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

VEEV and alphavirus belong to the togavirus family, which are single-stranded, positive sense RNA viruses. The genomes of VEEV and alphavirus are 11.5 kb, and the 5' two-thirds of RNA encodes two non-structural proteins, which are cleaved into three or four peptides required for RNA genome replication. The 3' one-third of the genomes encodes a structural protein that is cleaved into three mature peptides (C, E2 and E1) by proteases (9) . In the first large gene of VEEV and some alphaviruses, a stop codon (UGA) is present downstream of the coding sequence of mature peptide nsP3. The translation stops at this UGA codon on most mRNA. However, for a small percentage of mRNA, translational read-through occurs at this stop codon, an arginine or another residue is incorporated at this position and the translation is extended to the next stop codon (9, 19, 20) . A larger non-structural protein is synthesized because of the translational read-through and one additional mature peptide (nsP4) is translated. The mature peptide cleavage sites are identified based on the alignments between the polyprotein and the homologs in the mature peptide database. Once the junction region is located between two consecutive mature peptides, the conserved signature sequences next to the cleavage sites are used to identify the exact position of the cleavage. The conserved signature sequences were documented in literature (9) .