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

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

To demonstrate the applicability of this method, we first considered Andean potato latent virus that contains a known overlapping gene. Andean potato latent virus is a positivesense single-stranded RNA virus (family Tymoviridae) in which the I870_gp1 gene, that encodes the putative The expected ORF length based on codon composition is calculated. ORFs longer than expected by random chance are identified. The expected ORF length is estimated by one of three tests. For the codon permutation test (B) the codon sequence on the original frame is permuted and ORF lengths on alternative reading frames measured for each permutation. For the synonymous mutation test (C), codons that preserve the original amino acid sequence are randomly generated and the length of ORFs on alternative reading frames subsequently measured (note that codon replacement is not restricted to the example mutations shown in the figure, all of which occur in the third nucleotide positions, and that codon replacement with the original codon is also possible). The third test requires both the codon permutation test and the synonymous mutation test P values to be below some cut-off value.