title: iROS-gPseKNC: Predicting replication origin sites in DNA by incorporating dinucleotide position-specific propensity into general pseudo nucleotide composition.
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.
authors.affiliation: Computer Department, Jing-De-Zhen Ceramic Institute, Jing-De-Zhen, 333403, China.|Information School, ZheJiang Textile and Fashion College, NingBo, 315211, China.|Gordon Life Science Institute, Boston, Massachusetts, 02478, USA.
authors.forename: Xuan
authors.initials: X
authors.lastname: Xiao
authors.affiliation: Computer Department, Jing-De-Zhen Ceramic Institute, Jing-De-Zhen, 333403, China.
authors.forename: Han-Xiao
authors.initials: HX
authors.lastname: Ye
authors.affiliation: School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
authors.forename: Zi
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Computer Department, Jing-De-Zhen Ceramic Institute, Jing-De-Zhen, 333403, China.
authors.forename: Jian-Hua
authors.initials: JH
authors.lastname: Jia
authors.affiliation: Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, 21589, Saudi Arabia.|Gordon Life Science Institute, Boston, Massachusetts, 02478, USA.
authors.forename: Kuo-Chen
authors.initials: KC
authors.lastname: Chou
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D018741:Replication Origin / Q000235:genetics*; D012984:Software
keywords: general pseudo nucleotide composition; iROS-gPseKNC; origin of replication; position-specific dinucleotide propensity; random forest