Oncotarget

Research Papers:

iOri-Human: identify human origin of replication by incorporating dinucleotide physicochemical properties into pseudo nucleotide composition

Chang-Jian Zhang, Hua Tang, Wen-Chao Li, Hao Lin, Wei Chen and Kuo-Chen Chou _

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Oncotarget. 2016; 7:69783-69793. https://doi.org/10.18632/oncotarget.11975

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Abstract

Chang-Jian Zhang1, Hua Tang2, Wen-Chao Li1, Hao Lin1,4, Wei Chen1,3,4, Kuo-Chen Chou1,3,4

1Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China

2Department of Pathophysiology, Southwest Medical University, Luzhou, 646000, China

3Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, 063000, China

4Gordon Life Science Institute, Boston, MA, 02478, USA

Correspondence to:

Hao Lin, email: hlin@gordonlifescience.org, hlin@uestc.edu.cn

Wei Chen, email: greatchen@ncst.edu.cn

Kuo-Chen Chou, email: kcchou@gordonlifescience.org

Keywords: human DNA, origin of replication, pseudo k-tuple nucleotide composition, physicochemical properties of dinucleotides

Received: July 06, 2016     Accepted: September 06, 2016     Published: September 12, 2016

ABSTRACT

The initiation of replication is an extremely important process in DNA life cycle. Given an uncharacterized DNA sequence, can we identify where its origin of replication (ORI) is located? It is no doubt a fundamental problem in genome analysis. Particularly, with the rapid development of genome sequencing technology that results in a huge amount of sequence data, it is highly desired to develop computational methods for rapidly and effectively identifying the ORIs in these genomes. Unfortunately, by means of the existing computational methods, such as sequence alignment or kmer strategies, it could hardly achieve decent success rates. To address this problem, we developed a predictor called “iOri-Human”. Rigorous jackknife tests have shown that its overall accuracy and stability in identifying human ORIs are over 75% and 50%, respectively. In the predictor, it is through the pseudo nucleotide composition (an extension of pseudo amino acid composition) that 96 physicochemical properties for the 16 possible constituent dinucleotides have been incorporated to reflect the global sequence patterns in DNA as well as its local sequence patterns. Moreover, a user-friendly web-server for iOri-Human has been established at http://lin.uestc.edu.cn/server/iOri-Human.html, by which users can easily get their desired results without the need to through the complicated mathematics involved.


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