BACKGROUND: 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.
RESULTS: 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.
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 
oriCs in both bacterial and archaeal genomes.