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

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 eit...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: David S. H. Chew, Ming-Ying Leung, Kwok Pui Choi
• Keywords: BMCBI 2007, Excursion Method, Many Computational Methods, Replication Origins