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

Tcherepanov, Vasily; Ehlers, Angelika; Upton, Chris

90-94% similar, 22 genes were 85-89% similar, 16 genes were 80-84% similar, 11 genes were 75-79% similar, 14 genes were 70-74% similar and 59 genes were <70% similar. This information is available from the Statistics menu within GATU. With a minimum threshold of 60% aa similarity between the reference gene and the target ortholog, 1063 ORFs (96%) were accepted automatically by GATU and a further 24 were accepted from the reference genome after reviewing data in the Unassigned ORF table. Although annotation of bacterial genomes is outside of our area of expertise, another 29 ORFs that were not annotated in the reference genome were added from the Unassigned-ORF table to the target genome based on their similarity to genes in the NCBI nr database. In total, we were able to annotate the C. pneumoniae TW183 genome with 1116 genes and gene fragments; in comparison, the GenBank file for this genome contains 1113 annotations (NC_005043). Additional file 1 [Additional file 1] contains two Excel spreadsheets showing a more detailed comparison of these annotations; in summary, our annotation performed with GATU added several annotations to the target that were not in its GenBank file and failed to predict a small number of short ORFs. However, such differences will arise whenever two authors annotate a genome using different processes and standards; the discrepancies seen here represent less than 10% of the total genes, indicating a high level of consistency between the two annotations.