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Open Access Research article

AT excursion: a new approach to predict replication origins in viral genomes by locating AT-rich regions

David SH Chew1*, Ming-Ying Leung2 and Kwok Pui Choi13

Author Affiliations

1 Department of Statistics and Applied Probability, National University of Singapore, Singapore 117546, Singapore

2 Department of Mathematical Sciences and Bioinformatics Program, The University of Texas at El Paso, TX 79968, USA

3 Department of Mathematics, National University of Singapore, Singapore 117543, Singapore

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BMC Bioinformatics 2007, 8:163  doi:10.1186/1471-2105-8-163

Published: 21 May 2007

Abstract

Background

Replication origins are considered important sites for understanding the molecular mechanisms involved in DNA replication. Many computational methods have been developed for predicting their locations in archaeal, bacterial and eukaryotic genomes. However, a prediction method designed for a particular kind of genomes might not work well for another. In this paper, we propose the AT excursion method, which is a score-based approach, to quantify local AT abundance in genomic sequences and use the identified high scoring segments for predicting replication origins. This method has the advantages of requiring no preset window size and having rigorous criteria to evaluate statistical significance of high scoring segments.

Results

We have evaluated the AT excursion method by checking its predictions against known replication origins in herpesviruses and comparing its performance with an existing base weighted score method (BWS1). Out of 43 known origins, 39 are predicted by either one or the other method and 26 origins are predicted by both. The excursion method identifies six origins not predicted by BWS1, showing that the AT excursion method is a valuable complement to BWS1. We have also applied the AT excursion method to two other families of double stranded DNA viruses, the poxviruses and iridoviruses, of which very few replication origins are documented in the public domain. The prediction results are made available as supplementary materials at [1]. Preliminary investigation shows that the proposed method works well on some larger genomes too.

Conclusion

The AT excursion method will be a useful computational tool for identifying replication origins in a variety of genomic sequences.