Journal
FEBS LETTERS
Volume 586, Issue 6, Pages 934-938Publisher
ELSEVIER SCIENCE BV
DOI: 10.1016/j.febslet.2012.02.034
Keywords
Origin of replication; Bendability; Cleavage intensity; Support vector machine
Funding
- The National Nature Scientific Foundation of China [61100092]
- The Scientific Research Startup Foundation of North China Coal Medical University [10101115]
- Foundation of Scientific and Technological Department of Hebei Province [11275532]
- The Scientific Research Foundation of Sichuan Province [2009JY0013]
- The Fundamental Research Funds for the Central Universities [ZYGX2009J081]
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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. (C) 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
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