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Human promoter recognition based on single nucleotide statistics and support vector machine ensemble
XU Wenxuan, ZHANG Li
Journal of Computer Applications    2015, 35 (10): 2808-2812.   DOI: 10.11772/j.issn.1001-9081.2015.10.2808
Abstract432)      PDF (756KB)(341)       Save
To efficiently discriminate the promoter in human genome, an algorithm for human promoter recognition based on single nucleotide statistics and Support Vector Machine (SVM) ensemble was proposed. Firstly, a gene dataset was divided into two subsets such as C-preferred and G-perferred subsets by using single nucleotide statistics. Secondly, DNA rigidity feature, word-based feature and CpG-island feature were extracted for each subset. Finally, these features were combined by using SVM ensemble learning. In addition, three ensemble ways were discussed, including single SVM ensemble, double-layer SVM ensemble and cascaded SVM ensemble. The experimental result shows that the proposed method can improve the sensitivity and specificity of human propoter recognition. Especially, the double-layer SVM ensemble can achieve the highest sensitivity of 79.51%, while the cascaded SVM ensemble has the highest specificity of 84.58%.
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