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

Tcherepanov, Vasily; Ehlers, Angelika; Upton, Chris

To initiate the process of transferring annotations using GATU, the user selects the reference genome (a file in Gen-Bank format) and the target genome to be annotated (a file in FASTA format) and then clicks the Annotate button; the reference and target genomes reside on the local/client machine. The program will then begin the annotation routine. The first step is to use each ORF in the reference genome as a query to search the target genome. GATU runs the following searches: 1) TBLASTN for intron-less genes and mature peptides (i.e. a final peptide or protein product following post-translational cleavage) and 2) BLASTN with the exons of intron-containing genes. The alignments returned by the BLAST searches are used, together with a list of putative ORFs (longer than the specified threshold), to infer potential annotations for the target genome.