title: Prediction of replication origins by calculating DNA structural properties.
abstract: In this study, we introduced two DNA structural characteristics, namely, bendability and hydroxyl radical cleavage intensity to analyze origin of replication (ORI) in the Saccharomyces cerevisiae genome. We found that both DNA bendability and cleavage intensity in core replication regions were significantly lower than in the linker regions. By using these two DNA structural characteristics, we developed a computational model for ORI prediction and evaluated the model in a benchmark dataset. The predictive performance of the jackknife cross-validation indicates that DNA bendability and cleavage intensity have the ability to describe core replication regions and our model is effective in ORI prediction.
authors.affiliation: Department of Physics, School of Sciences, Hebei United University, Tangshan, China. chenwei_imu@yahoo.com.cn
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.forename: Pengmian
authors.initials: P
authors.lastname: Feng
authors.forename: Hao
authors.initials: H
authors.lastname: Lin
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004261:DNA Replication; D030561:Databases, Nucleic Acid; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D018741:Replication Origin; D012441:Saccharomyces cerevisiae / Q000235:genetics
chemical_list: D004247:DNA