Gao Feng, Zhang Chun-Ting
Department of Physics, Tianjin University, Tianjin 300072, China.
BMC Bioinformatics. 2008 Feb 1;9:79. doi: 10.1186/1471-2105-9-79.
Chromosomal replication is the central event in the bacterial cell cycle. Identification of replication origins (oriCs) is necessary for almost all newly sequenced bacterial genomes. Given the increasing pace of genome sequencing, the current available software for predicting oriCs, however, still leaves much to be desired. Therefore, the increasing availability of genome sequences calls for improved software to identify oriCs in newly sequenced and unannotated bacterial genomes.
We have developed Ori-Finder, an online system for finding oriCs in bacterial genomes based on an integrated method comprising the analysis of base composition asymmetry using the Z-curve method, distribution of DnaA boxes, and the occurrence of genes frequently close to oriCs. The program can also deal with unannotated genome sequences by integrating the gene-finding program ZCURVE 1.02. Output of the predicted results is exported to an HTML report, which offers convenient views on the results in both graphical and tabular formats.
A web-based system to predict replication origins of bacterial genomes has been presented here. Based on this system, oriC regions have been predicted for the bacterial genomes available in GenBank currently. It is hoped that Ori-Finder will become a useful tool for the identification and analysis of oriCs in both bacterial and archaeal genomes.
染色体复制是细菌细胞周期中的核心事件。对于几乎所有新测序的细菌基因组而言，鉴定复制起点（oriC）都是必要的。然而，鉴于基因组测序的速度不断加快，当前可用的用于预测oriC的软件仍有诸多不足。因此，随着基因组序列的日益增多，需要改进软件以在新测序且未注释的细菌基因组中鉴定oriC。
我们开发了Ori-Finder，这是一个基于综合方法在细菌基因组中寻找oriC的在线系统，该综合方法包括使用Z曲线法分析碱基组成不对称性、DnaA框的分布以及靠近oriC的常见基因的出现情况。该程序还可以通过整合基因发现程序ZCURVE 1.02来处理未注释的基因组序列。预测结果输出到HTML报告中，该报告以图形和表格格式提供对结果的便捷查看。
本文介绍了一种基于网络的预测细菌基因组复制起点的系统。基于该系统，目前已对GenBank中可用的细菌基因组的oriC区域进行了预测。希望Ori-Finder将成为鉴定和分析细菌及古细菌基因组中oriC的有用工具。
