VIGOR

VIGOR predicts and annotates protein-coding genes and genome-specific features in small viral genomes to enable accurate viral gene annotation.

Key Features:

• Gene prediction: Identifies protein-coding regions, start and stop codons using sequence similarity searches against custom protein databases.
• Genome-specific feature detection: Detects frame shifts, ribosomal slippage, RNA editing, stop codon read-through (stop codon leakage), overlapping genes, and embedded genes.
• Mature peptide cleavage sites: Predicts mature peptide cleavage sites within viral polyproteins.
• High-throughput annotation: Supports high-throughput feature prediction and annotation for multiple viral genomes.
• Output files: Generates a gene prediction file, a complementary DNA (cDNA) file, an alignment file, and a detailed gene feature table suitable for GenBank submissions.

Scientific Applications:

• Coronaviruses, influenza, rhinovirus, rotavirus: Applied to predict and annotate genes and complex features in these viral genomes.
• Additional virus support: Extended to predict genes for measles virus, mumps virus, rubella virus, respiratory syncytial virus, alphavirus, Venezuelan equine encephalitis virus, norovirus, metapneumovirus, yellow fever virus, Japanese encephalitis virus, parainfluenza virus, and Sendai virus.
• Validation: Accuracy validated through testing on datasets of 27 to 240 viral genomes sourced from GenBank.

Methodology:

Analyzes viral genomic sequences in FASTA format using sequence similarity searches against custom protein databases and signature residues to identify and annotate gene features including RNA editing, stop codon read-through, and ribosomal slippage.