Table 1.

Analysing previous overlapping genes reports

Reference	Objective	Excluded genes	Accepted gene set	Annotation errors suggested
Fukuda et al., 1999 [11]Fukuda et al., 2003 [7]	Comparison study of overlapping genes in two Mycoplasma genomes. Study of overlapping genes in bacterial genomes	Homologous genes whose start codons was assigned differently and genes coding for hypothetical or putative proteins	Authentic ORFs, thus genes not annotated as hypothetical or putative proteins and conserved in COG database	Misprediction of the start codons
Rogozin et al., 2002 [12]	Study of non-coding DNA in prokaryotic genomes	Genes coding for hypothetical proteins and overlapping more than 90 bps	Gene pairs not annotated as hypothetical or putative proteins and conserved in COG database	Misprediction of start codons, falsely predicted genes and missed genes, frameshifts
Rogozin et al., 2002 [14]	Analysis of the purifying and directional selection in overlapping prokaryotic genes	Genes not conserved in COG database and neither co-directional nor divergent overlapping pairs nor overlapping gene pairs not conserved in two or more species	Convergent overlapping genes conserved in both the COG database and in two or more than two genomes	Misprediction of start codons (affecting co-directional and divergent overlaps) and loss of termination codons (affecting co-directional and convergent overlaps)
Johnson and Chisholm, 2004 [6]	Study of the properties of the overlapping genes in microbial genomes	Genes coding for hypothetical proteins	Gene pairs not annotated as hypothetical or putative proteins	Misidentification of coding sequences
Sakharkar et al., 2005 [13]	Comparison study of overlapping genes in two Rickettsia genomes	Genes coding for hypothetical proteins	Gene pairs not annotated as hypothetical or unknown proteins	Incorrectly annotated ORFs
Cock and Withworth, 2007 [15]	Study of the relative reading frame bias in Prokaryotic Two-component system genes which use to overlap	Genes with ambiguous locations	Two component system gene pairs well located in the chromosome	Invalid bacterial start codons or premature stop codons

Comparison of previous overlapping genes studies. Columns referring to the authors, the authors' objectives, the genes excluded from their study, the genes accepted for their study, and the misannotations which they suggest are present in prokaryotic chromosomes.