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Table 1 Analysing previous overlapping genes reports

From: Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?

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
  1. 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.