Skewed oligomers and origins of replication

被引：139

作者：

Salzberg, SL

Salzberg, AJ

Kerlavage, AR

Tomb, JF

机构：

[1] Inst Genom REs, Rockville, MD 20850 USA

[2] Johns Hopkins Univ, Dept Comp Sci, Baltimore, MD 21218 USA

[3] KPMG, Washington, DC 20036 USA

来源：

GENE | 1998年 / 217卷 / 1-2期

关键词：

comparative genomics; sequence analysis; computational methods;

D O I：

10.1016/S0378-1119(98)00374-6

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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. (C) 1998 Elsevier Science B.V. All rights reserved.

引用

页码：57 / 67

页数：11

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