Pseudogenes in prokaryotes. (a) Procedure for assigning pseudogenes. The flow chart shows the steps in identifying pseudogenes in 64 prokaryote genomes. The steps include: separate intergenic regions from coding sequence (hypothetical ORFs were excluded); six-frame FastX search on intergenic regions for pseudogene candidates; quality control to reduce false-positive results introduced by artificial disablement or by different codon usage. (b) The occurrence of relative disablement positions in pseudogenes, which were normalized on a 100-residue scale based on ratios of the distances from starting residues to disablements to the length of pseudogenes. The yellow bars indicate the distribution of disablement positions before the last quality-control step and the green bars show the distribution after minimizing false-positive pseudogenes.
Liu et al. Genome Biology 2004 5:R64 doi:10.1186/gb-2004-5-9-r64