A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences

Schlub, Timothy E; Buchmann, Jan P; Holmes, Edward C

Our results do indicate that antisense ORFs are present at levels higher than currently expected. This does not necessarily mean that a transcribed protein is functional, although its presence may be indicative of some functional benefit, such as regulating expression by diverting ribosomes (Pelechano and Steinmetz 2013; Beltran and Garcia de Herreros 2016) . Importantly, our method's high detection of antisense ORFs are in contrast to other bioinformatic screening methods which have been shown to have poor sensitivity to antisense ORFs by computer simulations. This is because synonymous mutations in frame þ0 impact the reverse complementary frame (specifically frame Àc2) much less than other reading frames (Mir and Schober 2014) . Although this feature would impact the sensitivity of our synonymous mutation test, as it would for all current methods, the codon permutation test will not impacted by this, and could be used in isolation when specifically screening for antisense ORFs.