Salzberg S L, Salzberg A J, Kerlavage A R, Tomb J F
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
Gene. 1998 Sep 14;217(1-2):57-67. doi: 10.1016/s0378-1119(98)00374-6.
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 sequences 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.
原核生物基因组中假定的复制起点可通过一种新方法来定位，该方法能找到其方向在起点周围优先发生偏斜的短寡聚物。偏斜寡聚物方法已被证明适用于所有细菌基因组以及迄今为止已测序的三个古菌基因组之一，在大多数情况下证实了已知或预测的起点，在三个案例（幽门螺杆菌、嗜热自养甲烷杆菌和集胞藻属）中还提示了先前未知的起点。在许多情况下，保守基因和核苷酸基序的存在证实了这些预测。本文描述了一种用于寻找这些偏斜七碱基和八碱基序列的算法，以及一种结合来自多个偏斜寡聚物的证据以准确定位复制起点的方法。文中还讨论了偏斜寡聚物现象的可能解释。对于为何一些细菌基因组含有数百个高度偏斜的寡聚物，而另一些仅含有少数几个，也给出了解释。
