VIGOR, an annotation program for small viral genomes

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

The National Institute of Allergy and Infectious Diseases (NIAID) funds a Genomic Sequencing Center for Infectious Diseases (GSCID) at the J. Craig Venter Institute (JCVI). One of the goals of the GSCID is high throughput sequencing of various viral pathogens. The viral genome sequencing projects at JCVI have resulted in publication of more than 4000 influenza virus genomes from clinical and animal reservoir specimens, and hundreds of coronavirus and rotavirus sequences. Prediction of protein coding genes encoded in these viral genomes is a critical step to understanding these pathogenic viruses. In order to have a flexible, accurate gene prediction tool for utilization in high throughput viral genome sequencing projects, we developed a viral annotation program, VIGOR (Viral Genome ORF Reader). VIGOR uses a similarity-based approach to detect open reading frames (ORF) in various viral genomes by similarity searches against custom reference protein sequence databases. VIGOR takes into account differences between the genomic structures of viral taxonomic groups. VIGOR is tailored for the designated viruses with complex gene features such as splicing and frame-shifting, and it is able to predict genes accurately in influenza (group A, B, and C), coronavirus (including SARS coronavirus), rhinovirus, and rotavirus genomes. It was also designed to assign function to the predicted ORFs and genotype influenza viruses. In addition to gene prediction, VIGOR can also be used as a tool to validate sequence accuracy and completeness during the genome finishing process.