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

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

Herein, we present a new statistical method for detecting overlapping genes in different reading frames that relies on only a single nucleotide sequence of a gene or genome. We apply this method to a large scale computational screening of all available (linear) RNA virus genomes. The method estimates the theoretical expected length of ORFs before a stop codon is reached in all reading frames within an established gene. If an ORF exists of much greater length than predicted by this expected length, then we surmise that there has been selection against the accumulation of stop codons that shorten the putative ORF. We conclude that this constitutes evidence that the ORF in question provides functional benefit to the virus. Despite its simplicity, we show that this method is a powerful way to detect functional overlapping genes that can be readily applied to large scale computational screening of all known viruses and to viruses newly discovered through metagenomics.