Deshayes_2007_Genome.Biol_8_R20

BACKGROUND In silico analysis has shown that all bacterial genomes contain a low percentage of ORFs with undetected frameshifts and in-frame stop codons These interrupted coding sequences ICDSs may really be present in the organism or may result from misannotation based on sequencing errors The reality or otherwise of these sequences has major implications for all subsequent functional characterization steps including module prediction comparative genomics and high-throughput proteomic projects RESULTS We show here using Mycobacterium smegmatis as a model species that a significant proportion of these ICDSs result from sequencing errors We used a resequencing procedure and mass spectrometry analysis to determine the nature of a number of ICDSs in this organism We found that 28 of the 73 ICDSs investigated correspond to sequencing errors CONCLUSION The correction of these errors results in modification of the predicted amino acid sequences of the corresponding proteins and changes in annotation We suggest that each bacterial ICDS should be investigated individually to determine its true status and to ensure that the genome sequence is appropriate for comparative genomics analyses.