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. 2008 Feb 1:9:79.
doi: 10.1186/1471-2105-9-79.

Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes

Feng Gao  1 , Chun-Ting Zhang
Affiliations

Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes

Feng Gao et al. BMC Bioinformatics. .

Abstract

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.

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Figures

Figure 1
Figure 1
A typical example of the output results obtained by Ori-Finder. (A) The information of genome and oriC region for Escherichia coli K12 as an HTML table. (B) The integrated plot as a PNG figure for the original sequence and (C) the integrated plot as a PNG figure for the rotated sequence, displaying the obtained results, such as general genome information, four disparity curves, distribution of DnaA boxes, locations of putative indicator genes and the predicted oriC region. Note that the coordinate origin of the rotated sequence begins and ends in the maximum of the GC disparity curve.
Figure 2
Figure 2
The procedure of Ori-Finder to identify oriC regions. Flow chart schematically showing the procedure to identify oriC regions by Ori-Finder.
See this image and copyright information in PMC

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