Cited by 375Machine Learning in BioinformaticsGenomics and Chromatin DynamicsFractal and DNA sequence analysis

Inuc-pseknc: A sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition

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Guo, Shou-Hui, Deng, En-Ze, Xu, Li-Qin, Ding, Hui, Lin, Hao, Chen, Wei, Chou, Kuo-Chen·2014·Bioinformatics

Abstract

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. Availability: A user-friendly web-server, iNuc-PseKNC is freely accessible at http://lin.uestc.edu.cn/server/iNuc-PseKNC. Contact: hlin@uestc.edu.cn, wchen@gordonlifescience.org, kcchou@gordonlifescience.org Supplementary information: Supplementary data are available at Bioinformatics online.

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Crossref · 10.1093/bioinformatics/btu083

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Authors
Guo, S.-H., Deng, E.-Z., Xu, L.-Q., Ding, H., Lin, H., Chen, W., & Chou, K.-C.
Affiliations
  • University of Electronic Science and Technology of China (CN)
  • 1 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, 2Gordon Life Science Institute, Belmont, Massachusetts, USA, 3Department of Physics, School of Sciences, Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China and 4Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
Corresponding author
  • Lin, Hao
  • Chen, Wei
  • Chou, Kuo-Chen
Venue
Bioinformatics
Published
2014-02-06
Volume
30
Issue
11
Pages
1522-1529
ISSN
  • 1367-4803 (ISSN-L)
  • 1367-4811
OpenAlex
W2139166279
Cited by
375
References
80
Citations by year
2026: 3 · 2025: 4 · 2024: 17 · 2023: 8 · 2022: 12 · 2021: 20 · 2020: 20 · 2019: 32 · 2018: 53 · 2017: 33 · 2016: 57 · 2015: 65 · 2014: 51
FWCI
28.14
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Bioinformatics (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
Keywords
nucleosome positioning, sequence-based prediction, Caenorhabditis elegans genome, Drosophila melanogaster genome, web server
MeSH terms
Animals, DNA, Drosophila melanogaster, Humans, Nucleosomes, Nucleotides, Software, Genome, Caenorhabditis elegans, Sequence Analysis, DNA, Genomics

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