Recognition for avian influenza virus proteins based on support vector machine and linear discriminant analysis

GuiZhao Liang; ZeCong Chen; ShanBin Yang; Hu Mei; Yuan Zhou; Li Yang; Peng Zhou; ShengXi Yang; Mao Shu; ChunYang Liao; ShiRong Wu; GenRong Li; Liu He; JianKun Gao; MengYu Gan; DeJing Li; GuoPing Chen; GuiXue Wang; Sha Long; JuHua Jing; XiaoLin Zheng; Hui Zeng; QiaoXia Zhang; MengJun Zhang; Qi Yang; FeiFei Tian; JianBo Tong; JiaoNa Wang; YongHong Liu; Bo Li; LiangJia Qiu; ShaoXi Cai; Na Zhao; Yan Yang; XiaLi Su; Jian Song; MeiXia Chen; XueJiao Zhang; JiaYing Sun; JingWei Li; GuoHua Chen; Gang Chen; Jie Deng; ChuanYou Peng; WanPing Zhu; LuoNan Xu; YuQuan Wu; LiMin Liao; Zhi Li; Jun Li; DaJun Lu; QinLiang Su; ZhengHu Huang; Ping Zhou; ZhiLiang Li

doi:10.1007/s11426-008-0006-7

Recognition for avian influenza virus proteins based on support vector machine and linear discriminant analysis

Sci China B Chem. 2008;51(2):166-170. doi: 10.1007/s11426-008-0006-7.

Authors

GuiZhao Liang^{1

2

3}, ZeCong Chen^{1

2}, ShanBin Yang^{1

2}, Hu Mei^{2

3}, Yuan Zhou^{2

3}, Li Yang^{2

3}, Peng Zhou^{1

3}, ShengXi Yang¹, Mao Shu^{1

3}, ChunYang Liao^{1

2}, ShiRong Wu^{1

2}, GenRong Li^{2

3}, Liu He^{2

3}, JianKun Gao^{2

3}, MengYu Gan^{1

2

3}, DeJing Li^{1

2}, GuoPing Chen^{2

3}, GuiXue Wang^{2

3}, Sha Long^{2

3}, JuHua Jing^{2

3}, XiaoLin Zheng^{2

3}, Hui Zeng^{1

2}, QiaoXia Zhang^{1

2}, MengJun Zhang^{1

2}, Qi Yang^{1

2}, FeiFei Tian^{2

3}, JianBo Tong^{1

2}, JiaoNa Wang¹, YongHong Liu^{1

2

3}, Bo Li¹, LiangJia Qiu^{2

3}, ShaoXi Cai^{2

3}, Na Zhao^{1

2

3}, Yan Yang^{1

2

3}, XiaLi Su^{2

3}, Jian Song^{1

2}, MeiXia Chen^{1

2}, XueJiao Zhang^{1

2}, JiaYing Sun^{1

2}, JingWei Li^{1

2

3}, GuoHua Chen^{1

2}, Gang Chen^{1

4}, Jie Deng^{1

2

3}, ChuanYou Peng^{1

2}, WanPing Zhu¹, LuoNan Xu^{1

2

3}, YuQuan Wu^{1

2}, LiMin Liao^{1

2}, Zhi Li^{1

2}, Jun Li¹, DaJun Lu¹, QinLiang Su¹, ZhengHu Huang^{1

2}, Ping Zhou^{1

2}, ZhiLiang Li^{1

2}

Affiliations

¹ College of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400044 China.
² Key Laboratory for Biomechanics and Tissue Engineering under Ministry of Education at Chongqing University, Chongqing, 400044 China.
³ College of Bioengineering, Chongqing University, Chongqing, 400044 China.
⁴ Technology Centre for Life Sciences and Biotechnology, Singapore Polytechnic, Singapore, 139651 Singapore.

Abstract

Total 200 properties related to structural characteristics were employed to represent structures of 400 HA coded proteins of influenza virus as training samples. Some recognition models for HA proteins of avian influenza virus (AIV) were developed using support vector machine (SVM) and linear discriminant analysis (LDA). The results obtained from LDA are as follows: the identification accuracy (R _ia) for training samples is 99.8% and R _ia by leave one out cross validation is 99.5%. Both R _ia of 99.8% for training samples and R _ia of 99.3% by leave one out cross validation are obtained using SVM model, respectively. External 200 HA proteins of influenza virus were used to validate the external predictive power of the resulting model. The external R _ia for them is 95.5% by LDA and 96.5% by SVM, respectively, which shows that HA proteins of AIVs are preferably recognized by SVM and LDA, and the performances by SVM are superior to those by LDA.

Keywords: HA protein; avian influenza virus (AIV); linear discriminant analysis (LDA); support vector machine (SVM).