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Background  Chromosomal replication is the central event in the bacterial cell cycle. Identification of replication origins ( oriC s) is necessary for almost all newly sequenced bacterial genomes. Given the increasing pace of genome sequencing, the current available software for predicting  oriC s, however, still leaves much to be desired. Therefore, the increasing availability of genome sequences calls for improved software to identify  oriC s in newly sequenced and unannotated bacterial genomes.    Results  We have developed Ori-Finder, an online system for finding  oriC s 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  oriC s. 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.    Conclusion  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  oriC s in both bacterial and archaeal genomes.

Ori-Finder: A web-based system for finding oriC s in unannotated bacterial genomes