VIGOR - VIRAL GENOME ORF READER

About VIGOR

The JCVI Genomic Sequencing Center for Infectious Diseases (GSCID) at The J. Craig Venter Institute is sponsored by the National Institute of Allergy and Infectious Diseases and is tasked with conducting high throughput sequencing of various infectious disease causing viruses including influenza virus, coronavirus, SARS coronavirus, rotavirus, rhinovirus, measles virus, mumps virus, rubella virus, metapneumovirus, norovirus, respiratory syncytial virus (RSV), Venezuelan equine encephalitis virus (VEEV), parainfluenza virus, yellow fever virus, Japenese encephalitis virus, West Nile virus, Dengue virus and others.

We developed a gene prediction program for small viral genomes called Viral Genome ORF Reader (VIGOR) to support high throughput feature prediction and annotation. VIGOR employs an extrinsic strategy and boasts sensitivity and specificity greater than 98% for the RNA viral genomes we tested. Genome-specific features identified by VIGOR include frame shifts, ribosomal slippage, RNA editing, stop codon read-through, overlapping genes, embedded genes, and mature peptide cleavage sites. Genotyping capability for influenza and rotavirus is built into the program.

The prediction software has been incorporated into JCVI's post-sequencing production pipeline for performing high throughput annotation and closure validation. The program is made available for public use here. The software is described in Shiliang Wang, Jaideep P. Sundaram, David Spiro, 2010, and Shiliang Wang, Jaideep P. Sundaram and Timothy B. Stockwell, 2012.

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