We extract some physical and chemical features re-lated to the occurrence of single nucleotide polymorphism （SNP） from three groups of sliding windows around SNP site,and then make the predictions about accuracy by ...We extract some physical and chemical features re-lated to the occurrence of single nucleotide polymorphism （SNP） from three groups of sliding windows around SNP site,and then make the predictions about accuracy by using radial basis function （RBF） networks. The result of the forward sliding windows sug-gests that the accuracies and Matthews correlation coefficient （MCC values） ascend with the increasing of length of sliding windows. The accuracies range from 73.27 % to 80.69 %,and MCC values range from 0.465 to 0.614. The backward sliding windows and the sliding windows with fixed length three are de-signed to find the crucial sites related to SNP. The results imply that the occurrence possibility of SNP relies heavily on the above physical and chemical features of sites which are at a distance around 20 bases from the SNP site. Compared with the support vector machine （SVM）,our RBF network approach has achieved more satisfactory results.展开更多
基金Supported by Discipline-Crossing Research Foundation of Huazhong Agricultural University(2008XKJC006)the Fundamental Research Funds for the Central Universities of China
文摘We extract some physical and chemical features re-lated to the occurrence of single nucleotide polymorphism （SNP） from three groups of sliding windows around SNP site,and then make the predictions about accuracy by using radial basis function （RBF） networks. The result of the forward sliding windows sug-gests that the accuracies and Matthews correlation coefficient （MCC values） ascend with the increasing of length of sliding windows. The accuracies range from 73.27 % to 80.69 %,and MCC values range from 0.465 to 0.614. The backward sliding windows and the sliding windows with fixed length three are de-signed to find the crucial sites related to SNP. The results imply that the occurrence possibility of SNP relies heavily on the above physical and chemical features of sites which are at a distance around 20 bases from the SNP site. Compared with the support vector machine （SVM）,our RBF network approach has achieved more satisfactory results.
