SUMMARY: 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.
AnagnostopoulosC.,
PiggotP. J.,
HochJ. A.1993; The genetic map of Bacillus subtilis
. In Bacillus and Other Gram-Positive Bacteria: Biochemistry, Physiology and Molecular Genetics pp 425–461 Edited by
SonensheinA. L.,
HochJ. A.,
LosickR.
Washington, DC: American Society for Microbiology;
CosminaP.,
RodriguezF., de FerraF.,
GrandiG.,
PeregoM.,
VenemaG.,
van SinderenD.1993; Sequence and analysis of the genetic locus responsible for surfactin synthesis in Bacillus subtilis
. Mol Microbiol 8:821–831
FumaS.,
FujishimaY.,
CorbellN.,
D’SouzaC.,
NakanoM. M.,
ZuberP.,
YamaneK.1993; Nucleotide sequence of 5’ portion of srf A that contains the region required for competence es tablishment in Bacillus subtilis
. Nucleic Acids Res 21:93–97
KrawetzS. A.1989; Sequence errors described in GenBank: a means to determine the accuracy of DNA sequence interpretation. Nucleic Acids Res 17:3951–3956
MizusawaS.,
NishimuraS.,
SelaF.1986; Improvement of the dideoxy chain termination method of DNA sequencing by use of deoxy-7-deazaguanosine triphosphate in place of dGTP. Nucleic Acids Res 14:1319–1324
RychlikW.,
RhoadsR. E.1990; A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing, and in vitro amplification of DNA. Nucleic Acids Res 17:8543–8551
SallesC.,
CreancierL.,
ClaverysJ. P.,
MejeanV.1992; The high level streptomycin gene from Streptococcus pneumoniae is a homolog of the ribosomal protein S12 gene from Escherichia coli
. Nucleic Acids Res 20: 6103
ZimmermannJ.,
VossH.,
SchwagerC.,
StegemannJ.,
ErfleH.,
StuckyK.,
KristensenT.,
AnsorgeW.1990; A simplified protocol for fast plasmid DNA sequencing. Nucleic Acids Res 18:1067