TY - JOUR
T1 - Skewed oligomers and origins of replication
AU - Salzberg, Steven L.
AU - Salzberg, Alan J.
AU - Kerlavage, Anthony R.
AU - Tomb, Jean Francois
N1 - Funding Information:
SLS is supported in part by NIH Grant K01-HG00022-1 and by NSF grant IRI-9530462. The authors thank O. White, C.M. Fraser, R.D. Fleischmann, H.O. Smith, and J.C. Venter for thoughtful comments on the manuscript.
PY - 1998/9/14
Y1 - 1998/9/14
N2 - The putative origin of replication in prokaryotic genomes can be located by a new method that finds short oligomers whose orientation is preferentially skewed around the origin. The skewed oligomer method is shown to work for all bacterial genomes and one of three archaeal genomes sequenced to date, confirming known or predicted origins in most cases and in three cases (H. pylori, M. thermoautotrophicum, and Synechocystis sp.), suggesting origins that were previously unknown. In many cases, the presence of conserved genes and nucleotide motifs confirms the predictions. An algorithm for finding these skewed seven-base and eight-base sequences is described, along with a method for combining evidence from multiple skewed oligomers to accurately locate the replication origin. Possible explanations for the phenomenon of skewed oligomers are discussed. Explanations are presented for why some bacterial genomes contain hundreds of highly skewed oligomers, whereas others contain only a handful.
AB - The putative origin of replication in prokaryotic genomes can be located by a new method that finds short oligomers whose orientation is preferentially skewed around the origin. The skewed oligomer method is shown to work for all bacterial genomes and one of three archaeal genomes sequenced to date, confirming known or predicted origins in most cases and in three cases (H. pylori, M. thermoautotrophicum, and Synechocystis sp.), suggesting origins that were previously unknown. In many cases, the presence of conserved genes and nucleotide motifs confirms the predictions. An algorithm for finding these skewed seven-base and eight-base sequences is described, along with a method for combining evidence from multiple skewed oligomers to accurately locate the replication origin. Possible explanations for the phenomenon of skewed oligomers are discussed. Explanations are presented for why some bacterial genomes contain hundreds of highly skewed oligomers, whereas others contain only a handful.
KW - Comparative genomics
KW - Computational methods
KW - Sequence analysis
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U2 - 10.1016/S0378-1119(98)00374-6
DO - 10.1016/S0378-1119(98)00374-6
M3 - Article
C2 - 9795135
AN - SCOPUS:0032517137
SN - 0378-1119
VL - 217
SP - 57
EP - 67
JO - Gene
JF - Gene
IS - 1-2
ER -