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Prediction of replication origins by calculating DNA structural properties

In this study, we introduced two DNA structural characteristics, namely, bendability and hydroxyl radical cleavage intensity to analyze origin of replication (ORI) in the genome. We found that both DNA bendability and cleavage intensity in core replication regions were significantly lower than in th... Full description

Journal Title: FEBS Letters 23 March 2012, Vol.586(6), pp.934-938
Main Author: Chen, Wei
Other Authors: Feng, Pengmian , Lin, Hao
Format: Electronic Article Electronic Article
Language:
Subjects:
ID: ISSN: 0014-5793 ; E-ISSN: 1873-3468 ; DOI: 10.1016/j.febslet.2012.02.034
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recordid: wj10.1016/j.febslet.2012.02.034
title: Prediction of replication origins by calculating DNA structural properties
format: Article
creator:
  • Chen, Wei
  • Feng, Pengmian
  • Lin, Hao
subjects:
  • Origin Of Replication
  • Bendability
  • Cleavage Intensity
  • Support Vector Machine
ispartof: FEBS Letters, 23 March 2012, Vol.586(6), pp.934-938
description: In this study, we introduced two DNA structural characteristics, namely, bendability and hydroxyl radical cleavage intensity to analyze origin of replication (ORI) in the 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. ► DNA bendability and cleavage intensity were analyzed in replication regions. ► Structural differences were observed between replication regions and linker regions. ► A novel computational model was proposed for replication origin prediction.
language:
source:
identifier: ISSN: 0014-5793 ; E-ISSN: 1873-3468 ; DOI: 10.1016/j.febslet.2012.02.034
fulltext: fulltext
issn:
  • 0014-5793
  • 00145793
  • 1873-3468
  • 18733468
url: Link


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subjectOrigin Of Replication ; Bendability ; Cleavage Intensity ; Support Vector Machine
descriptionIn this study, we introduced two DNA structural characteristics, namely, bendability and hydroxyl radical cleavage intensity to analyze origin of replication (ORI) in the 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. ► DNA bendability and cleavage intensity were analyzed in replication regions. ► Structural differences were observed between replication regions and linker regions. ► A novel computational model was proposed for replication origin prediction.
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titlePrediction of replication origins by calculating DNA structural properties
descriptionIn this study, we introduced two DNA structural characteristics, namely, bendability and hydroxyl radical cleavage intensity to analyze origin of replication (ORI) in the 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. ► DNA bendability and cleavage intensity were analyzed in replication regions. ► Structural differences were observed between replication regions and linker regions. ► A novel computational model was proposed for replication origin prediction.
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abstractIn this study, we introduced two DNA structural characteristics, namely, bendability and hydroxyl radical cleavage intensity to analyze origin of replication (ORI) in the 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. ► DNA bendability and cleavage intensity were analyzed in replication regions. ► Structural differences were observed between replication regions and linker regions. ► A novel computational model was proposed for replication origin prediction.
doi10.1016/j.febslet.2012.02.034
pages934-938
date2012-03-23