Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Research article

Wavelet to predict bacterial ori and ter: a tendency towards a physical balance

Jiuzhou Song1, Antony Ware2 and Shu-Lin Liu13*

Author Affiliations

1 Departments of Microbiology and Infectious Diseases, University of Calgary, Calgary, Canada

2 Mathematics and Statistics, University of Calgary, Calgary, Canada

3 Department of Microbiology, Peking University School of Basic Medical Sciences, Beijing, China

For all author emails, please log on.

BMC Genomics 2003, 4:17  doi:10.1186/1471-2164-4-17

Published: 5 May 2003

Abstract

Background

Chromosomal DNA replication in bacteria starts at the origin (ori) and the two replicores propagate in opposite directions up to the terminus (ter) region. We hypothesize that the two replicores need to reach ter at the same time to maintain a physical balance; DNA insertion would disrupt such a balance, requiring chromosomal rearrangements to restore the balance. To test this hypothesis, we needed to demonstrate that ori and ter are in a physical balance in bacterial chromosomes. Using wavelet analysis, we documented GC skew, AT skew, purine excess and keto excess on the published bacterial genomic sequences to locate the turning (minimum and maximum) points on the curves. Previously, the minimum point had been supposed to correlate with ori and the maximum to correlate with ter.

Results

We observed a strong tendency of the bacterial chromosomes towards a physical balance, with the minima and maxima corresponding to the known or putative ori and ter and being about half chromosome separated in most of the bacteria studied. A nonparametric method based on wavelet transformation was employed to perform significance tests for the predicted loci.

Conclusions

The wavelet approach can reliably predict the ori and ter regions and the bacterial chromosomes have a strong tendency towards a physical balance between ori and ter.