VIGOR, an annotation program for small viral genomes

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

Although most viral genomes are relatively small compared to eukaryotic and prokaryotic genomes, the gene structure of viral genomes can be complex. For example, introns, alternative splicing, overlapping genes, and ribosomal slippage exist in many viral genomes. Thus an all purpose gene finder cannot be easily adapted for gene prediction across all virus families. However, if the genome scaffold and the gene features of a viral genome are well understood, a similarity-based gene prediction approach based on the curated gene repertoire for a specific virus genus with attention to particular recognition features, such as, splice sites and mature peptide cleavage sites can be adapted, and perform better than an ab initio gene finder.