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

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

Synplot2 is a commonly used bioinformatic approach to identify overlapping genes by detecting reduced variability at synonymous sites (Firth 2014) . Although powerful, this method is necessarily constrained by the requirement for multiple sequences of sufficient diversity to robustly detect overlapping genes. In contrast, our method requires only a single sequence, and can therefore be applied in many situations where Synplot2 would be inviable. Quantitative comparisons of sensitivity and false discovery between the methods are difficult, as the factors associated with sensitivity in Synplot2 (sequence diversity, recombination, and window size) are not present in our method. Therefore, to make this comparison informative, we apply our method to the Synplot2 validation data set (table 1 from Firth 2014) and report the results in table 2. This validation consists of 21 gene overlaps with a minimum overlap length of 108 nucleotides. We find that using a P value cut of value of 0.01, the codon permutation method, synonymous mutation method, and combined approach detects 12, 12, and 10 of the gene overlaps, respectively. These results are in agreement with our previous sensitivity estimates. For example, Figure 3 shows that the combined approach will have $50% sensitivity for overlaps of at least 100 nucleotides when a P value cut-off of 0.01 is used.