iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition. Motivation: 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.

References in zbMATH (referenced in 9 articles )

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  1. Jiao, Ya-Sen; Du, Pu-Feng: Predicting Golgi-resident protein types using pseudo amino acid compositions: approaches with positional specific physicochemical properties (2016)
  2. Yang, Lianping; Zhang, Xiangde; Fu, Haoyue; Yang, Chenhui: An estimator for local analysis of genome based on the minimal absent word (2016)
  3. Ali, Farman; Hayat, Maqsood: Classification of membrane protein types using voting feature interval in combination with Chou’s pseudo amino acid composition (2015)
  4. Aram, Reza Zohouri; Charkari, Nasrollah Moghadam: A two-layer classification framework for protein fold recognition (2015)
  5. Ju, Zhe; Cao, Jun-Zhe; Gu, Hong: iLM-2L: a two-level predictor for identifying protein lysine methylation sites and their methylation degrees by incorporating K-gap amino acid pairs into Chou’s general PseAAC (2015)
  6. Khan, Zaheer Ullah; Hayat, Maqsood; Khan, Muazzam Ali: Discrimination of acidic and alkaline enzyme using Chou’s pseudo amino acid composition in conjunction with probabilistic neural network model (2015)
  7. Kou, Gaoshan; Feng, Yonge: Identify five kinds of simple super-secondary structures with quadratic discriminant algorithm based on the chemical shifts (2015)
  8. Kumar, Ravindra; Srivastava, Abhishikha; Kumari, Bandana; Kumar, Manish: Prediction of $\beta$-lactamase and its class by Chou’s pseudo-amino acid composition and support vector machine (2015)
  9. Marrero-Ponce, Yovani; Contreras-Torres, Ernesto; García-Jacas, César R.; Barigye, Stephen J.; Cubillán, Néstor; Alvarado, Ysaías J.: Novel 3D bio-macromolecular bilinear descriptors for protein science: predicting protein structural classes (2015)