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

Tcherepanov, Vasily; Ehlers, Angelika; Upton, Chris

useful at this stage is JDotter, which can show an alignment of the genomes together with the whole genome dotplots [9] . With these data at hand, the user can now make an informed decision as to whether this putative ORF should be included in the target genome annotations. Given that the promoter regions and ORF start sites are similar, it is likely that protein translation of this mRNA would begin at the same position as in the reference genome, leading to the synthesis of a polypeptide only 12 aa in length. Therefore, this ORF should be omitted from the annotation even though, at first glance, it appears to be significant. Alternatively, the annotation could be accepted with the FRAG (fragment) designation; the user can select this by clicking in the relevant row of the Genetype column.