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

Tcherepanov, Vasily; Ehlers, Angelika; Upton, Chris

Of note, is that GATU allows the user to review the BLAST alignments together with the reference genes used in this process; for all the suggested annotations that are displayed in the Annotation window, links are provided to the search and alignment results. The overall annotation algorithm is shown in Figure 1 . For each reference gene tested, GATU takes the start and stop positions of the best BLAST match in the target genome; if necessary, it then extends the ends of this exon in both directions in the same reading frame until the nucleotide sequence contains a start or a stop codon. Exons in the reference genome that lack either a start or a stop codon are excluded from this process, along with mature peptides. The region found in this manner is translated into a peptide sequence; NEEDLE then generates a global alignment between this translated sequence and the corresponding protein from the reference genome. If the similarity score for the alignment exceeds the cut-off value for acceptance (which can be changed by selecting Preferences from the menu), the "Accept annotation" box for this gene will be pre-checked to simplify the process for the user.