Oncotarget

Research Papers:

iROS-gPseKNC: Predicting replication origin sites in DNA by incorporating dinucleotide position-specific propensity into general pseudo nucleotide composition

Xuan Xiao _, Han-Xiao Ye, Zi Liu, Jian-Hua Jia and Kuo-Chen Chou

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Oncotarget. 2016; 7:34180-34189. https://doi.org/10.18632/oncotarget.9057

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Abstract

Xuan Xiao1,2,5, Han-Xiao Ye1, Zi Liu3, Jian-Hua Jia1, Kuo-Chen Chou4,5

1Computer Department, Jing-De-Zhen Ceramic Institute, Jing-De-Zhen, 333403, China

2Information School, ZheJiang Textile and Fashion College, NingBo, 315211, China

3School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China

4Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, 21589, Saudi Arabia

5Gordon Life Science Institute, Boston, Massachusetts, 02478, USA

Correspondence to:

Xuan Xiao, email: xxiao@gordonlifescience.org, jdzxiaoxuan@163.com

Keywords: origin of replication, position-specific dinucleotide propensity, general pseudo nucleotide composition, random forest, iROS-gPseKNC

Received: March 02, 2016     Accepted: April 09, 2016     Published: April 27, 2016

ABSTRACT

DNA replication, occurring in all living organisms and being the basis for biological inheritance, is the process of producing two identical replicas from one original DNA molecule. To in-depth understand such an important biological process and use it for developing new strategy against genetics diseases, the knowledge of duplication origin sites in DNA is indispensible. With the explosive growth of DNA sequences emerging in the postgenomic age, it is highly desired to develop high throughput tools to identify these regions purely based on the sequence information alone. In this paper, by incorporating the dinucleotide position-specific propensity information into the general pseudo nucleotide composition and using the random forest classifier, a new predictor called iROS-gPseKNC was proposed. Rigorously cross–validations have indicated that the proposed predictor is significantly better than the best existing method in sensitivity, specificity, overall accuracy, and stability. Furthermore, a user-friendly web-server for iROS-gPseKNC has been established at http://www.jci-bioinfo.cn/iROS-gPseKNC, by which users can easily get their desired results without the need to bother the complicated mathematics, which were presented just for the integrity of the methodology itself.


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