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

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

We find that the three test (codon permutation, synonymous mutation, and combined) have similar sensitivities for P value cut-offs between 0.001 and 0.10, with the synonymous mutation generally having the highest sensitivity, followed by the codon permutation test and then the combined test ( fig. 3 , Table 1 ). However, for all three tests we also find that sensitivities are generally insufficient when the overlapping length is below 50 nucleotides in length (<17 codons), but improve considerably as the overlapping length increases above 50 nucleotides. Importantly, the three tests show The expected distribution of ORF lengths in frame 2þ (shaded area) calculated by permutation test, and the actual ORF lengths on frame 1þ (black dots). The known frameshifted gene, I870_gp1, was clearly identified using the permutation test as its length was much larger than that expected by chance alone (P < 0.0001). Schlub et al. . doi:10.1093/molbev/msy155 MBE considerable differences in false discovery rates, with the synonymous mutation tests showing the highest (worst) rates and the combined test with the lowest (best) rates. As the highest and lowest sensitivity tests (synonymous mutation and combined, respectively) are also the tests with the corresponding highest and lowest false discovery rates, we used the standard measure of a diagnostic tool-the area under the curve-to compare which test gave the best sensitivity and false discovery rate combinations. The area under the curve here will lie between 0 and 1, with a value of 0.5 indicating a screening tool of no benefit, and a value of 1 indicating a perfect screening tool with no error. Accordingly, we find that the combined test consistently has the best sensitivity and false discovery rate combinations across all minimum overlap lengths, with an area under the curve increasing from 0.59 to 0.89 as the minimum overlap length increases from 50 to 300 nucleotides (table 1). This demonstrates that the combined test is a successful screening tool with both high sensitivity and relatively low false discovery.