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

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

The sensitivity (true positive rate) is measured as the proportion of known overlapping genes within the downloaded reference genomes that are detected using our method. An ORF identified with our method was considered a true positive if it was located on the same reading frame and overlapped with a gene already annotated in the reference genome. As the sensitivity of our method will be dependent on the extent of overlap, we calculated the sensitivity for detecting previously annotated overlapping genes where the minimum nucleotide length of overlap is 1, 10, 20 50, 100, 150, 200, and 300 nucleotides. The false discovery rate calculation is more complex as the absence of an annotated overlapping gene does not exclude its biological presence so that distinguishing between false positives and new discoveries is not possible without extensive laboratory work. To overcome this, we conservatively estimated the false discovery rate of our tests by using the nonviable 3 0 -5 0 reading frames (À0, À1, À2, þc0, þc1, and þc2, supplementary material S1, Supplementary Material online) as a negative control. That is, as detected ORFs on these frames cannot be transcribed into proteins and are therefore false positives, they serve as an estimate to what proportion of detected ORFs on viable reading frames are similarly not functional.