Analysis of errors in finished DNA sequences: the surfactin operon of Bacillus subtilis as an example.
Increased productivity in DNA sequencing would not be valid without a straightforward detection and estimation of errors in finished sequences. The sequence of the surfactin operon from Bacillus subtilis was obtained by two different groups and by chance we were also working on the same chromosome region. Taking advantage of this situation we report in this paper, the number and nature of errors found in the overlapping part of the DNA sequences obtained by the three laboratories. The coincidence of some of the errors with compression in sequence ladders and with secondary DNA structures as well as the detection of frameshift errors using computer programs, are demonstrated. Finally we discuss the definition of a new sequencing strategy that might minimize both the error rate and the cost of sequencing.
Fabret
C
C
Laboratoire de Chimie Bactérienne, Marseille, France.
Quentin
Y
Y
Guiseppi
A
A
Busuttil
J
J
Haiech
J
J
Denizot
F
F
D016477:Artifacts; D001412:Bacillus subtilis / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics*; D001483:Base Sequence; D055666:Lipopeptides; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009876:Operon / Q000235:genetics*; D010456:Peptides, Cyclic; D016364:Reading Frames / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000191:economics / Q000379:methods*; D012984:Software
D001426:Bacterial Proteins; D055666:Lipopeptides; D010456:Peptides, Cyclic; C009365:surfactin peptide