iOri-Human: identify human origin of replication by incorporating dinucleotide physicochemical properties into pseudo nucleotide composition
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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
Hao Lin, email: [email protected], [email protected]
Wei Chen, email: [email protected]
Kuo-Chen Chou, email: [email protected]
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
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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