title: iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition.
abstract: BACKGROUND
  Nucleosome positioning participates in many cellular activities and plays significant roles in regulating cellular processes. With the avalanche of genome sequences generated in the post-genomic age, it is highly desired to develop automated methods for rapidly and effectively identifying nucleosome positioning. Although some computational methods were proposed, most of them were species specific and neglected the intrinsic local structural properties that might play important roles in determining the nucleosome positioning on a DNA sequence.
  
  
  RESULTS
  Here a predictor called 'iNuc-PseKNC' was developed for predicting nucleosome positioning in Homo sapiens, Caenorhabditis elegans and Drosophila melanogaster genomes, respectively. In the new predictor, the samples of DNA sequences were formulated by a novel feature-vector called 'pseudo k-tuple nucleotide composition', into which six DNA local structural properties were incorporated. It was observed by the rigorous cross-validation tests on the three stringent benchmark datasets that the overall success rates achieved by iNuc-PseKNC in predicting the nucleosome positioning of the aforementioned three genomes were 86.27%, 86.90% and 79.97%, respectively. Meanwhile, the results obtained by iNuc-PseKNC on various benchmark datasets used by the previous investigators for different genomes also indicated that the current predictor remarkably outperformed its counterparts.
  
  
  BACKGROUND
  A user-friendly web-server, iNuc-PseKNC is freely accessible at http://lin.uestc.edu.cn/server/iNuc-PseKNC.
authors: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.
authors: Shou-Hui
authors: SH
authors: Guo
authors: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.
authors: En-Ze
authors: EZ
authors: Deng
authors: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.
authors: Li-Qin
authors: LQ
authors: Xu
authors: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.
authors: Hui
authors: H
authors: Ding
authors: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi ArabiaKey Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.
authors: Hao
authors: H
authors: Lin
authors: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi ArabiaKey Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.
authors: Wei
authors: W
authors: Chen
authors: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi ArabiaKey Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China, Gordon Life Science Institute, Belmont, Massachusetts, USA, Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.
authors: Kuo-Chen
authors: KC
authors: Chou
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D004247:DNA / Q000737:chemistry; D004331:Drosophila melanogaster / Q000235:genetics; D016678:Genome; D023281:Genomics / Q000379:methods; D006801:Humans; D009707:Nucleosomes / Q000737:chemistry*; D009711:Nucleotides / Q000032:analysis; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D009707:Nucleosomes; D009711:Nucleotides; D004247:DNA