Prediction of replication origins by calculating DNA structural properties.

Wei Chen, Pengmian Feng, Hao Lin

Department of Physics, School of Sciences, Hebei United University, Tangshan, China. chenwei_imu@yahoo.com.cn

FEBS letters 2012 Mar 23

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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. Copyright Â© 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Citation

Wei Chen, Pengmian Feng, Hao Lin. Prediction of replication origins by calculating DNA structural properties. FEBS letters. 2012 Mar 23;586(6):934-8