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

Tcherepanov, Vasily; Ehlers, Angelika; Upton, Chris

In summary, GATU correctly transferred and automatically accepted annotation for 146 of 148 genes from the reference sheeppox genome to the target genome. The missing genes (2 copies of a gene in the terminal inverted repeats of the viral genome) encode a protein of only 36 aa and were subsequently detected by a TBLASTN search of the target genome. In further tests, 97% of the genes in rabbitpox virus (AY484669; a strain vaccinia virus) were correctly annotated by using vaccinia virus strain WR (NC_006998) as the reference genome, whereas 88% of the genes in rabbitpox virus were correctly annotated by using ectromelia virus (a different species in the same Orthopoxvirus genus) as reference (data not shown). It should be noted, however, that although duplicated genes, such as those in poxvirus terminal inverted repeats, are detected by GATU, the evaluation of paralogues requires special attention because GATU can only match a reference gene to the first BLAST hit that is found. GATU places other paralogues into the Unassigned-ORFs group where they can be reviewed by the annotator and manually added to the annotation.