VIGOR extended to annotate genomes for additional 12 different viruses

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

Twenty-seven complete MPV genomes were used to evaluate VIGOR. A total of 243 genes were detected by VIGOR, the same number of genes were annotated in GenBank. VIGOR predictions completely agreed with GenBank annotations for 235 genes. VIGOR detected internal stop codons in the coding regions of four genes and the truncated proteins were shorter than 95% of the reference protein length. VIGOR, therefore, categorized these four genes as pseudogenes. These genes were annotated as functional genes in GenBank. The start codons are the same as these predicted by VIGOR. The stop codons in GenBank of these genes are same as the internal stop codons detected by VIGOR. The other four cases, in which VIGOR gene predictions were not same as GenBank annotations, are the M2 ORF1 gene (M2-1). Two versions of M2-1 protein exist in GenBank protein database. The longer protein has five additional amino acids at the N-terminus. VIGOR always selects the longer protein to be the reference sequence. The upstream ATG was therefore selected as the start codon in these four genes. In the corresponding GenBank annotations, the downstream ATG were annotated as the start codons for these four genes.