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

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

The following notation is used to identify the different reading frames (supplementary material S1, Supplementary Material online): þ0 is the original reading frame; þ1 or þ2 is a frameshift of 1 or 2 nucleotides, respectively (5 0 to 3 0 transcription); À0, À1, or À2 a frameshift of 0, 1 or 2 nucleotides, respectively, after the coding sequence has been reversed (i.e. 3 0 to 5 0 transcription); þc0, þc1 or þc2 is a frameshift of 0, 1 or 2 nucleotides, respectively, on the complement of the coding sequence (3 0 to 5 0 transcription); and Àc0, Àc1 or -c2 is a frameshift of 0, 1 or 2 nucleotides, respectively, on the complement and reversed coding sequence (5 0 to 3 0 transcription). þ0, þ1, þ2, þc0, þc1, þc2 are considered the only viable reading frames as transcription on these frames occur in the 5 0 to 3 0 direction.