VIGOR, an annotation program for small viral genomes

Wang, Shiliang; Sundaram, Jaideep P; Spiro, David

VIGOR detects protein coding sequences based on similarity searches in conjunction with the known genome specific features for the particular viral genomes. Genes with introns, overlapping genes, and even the genes with a frameshift due to ribosomal slippage can be identified accurately because VIGOR includes these complex mechanisms in the processing for the designated genomes. Both the specificity and sensitivity of VIGOR for the tested genomes was greater than 99%. The same sets of viral genomes were tested for two existing universal viral gene predication methods, the specificity was between 31% and 95%, and the sensitivity was from 35% to 96%. VIGOR was designed to predict the mature peptides accurately for rhinovirus genomes and SARS coronavirus genomes, which is not applicable for the existing universal gene prediction tools. VIGOR can also conduct genotyping and assign function to the predicted protein, both of which are not capable for most available viral gene prediction tools. This userfriendly program is convenient for high throughput sequencing projects and for use by individual laboratories. If reference protein sequences can be collected, and genome specific features are added to VIGOR, this program can extend its capability to predict the protein coding genes in many other small viral genomes.