Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome

Tcherepanov, Vasily; Ehlers, Angelika; Upton, Chris

To complement the process of matching known genes in the reference genome to the target, it is necessary to search for potential ORFs in the target genome that have no obvious match in the reference genome. Such ORFs could be the result of additional sequences in the target genome, minor sequence differences in the reference genome resulting in the loss of a functional gene, errors in the original annotation, overlapping ORFs, or failure to use the first MET codon as the ORF start. All ORFs larger than the Cutoff size that have not been matched to a gene in the ref- Figure 3 List of ORFs automatically annotated by GATU. One ORF that was not detected in the target genome is highlighted in blue in the top panel of the main GATU window; the Accept button is not selected. There is no corresponding ORF in the bottom half of the panel representing the target genome.