Identification of bacteriophage virion proteins by the ANOVA feature selection and analysis
Identification of bacteriophage virion proteins by the ANOVA feature selection and analysis
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DOI：
10.1039/c4mb00316k
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发表时间：
2014-01-01
影响因子：
--
通讯作者：
Lin, Hao
中科院分区：
文献类型：
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作者：
Ding, Hui;Feng, Peng-Mian;Lin, Hao
噬菌体病毒粒子蛋白在宿主细菌细胞的命运中起着极其重要的作用。准确鉴定噬菌体病毒粒子蛋白对于了解其功能和阐明细菌细胞裂解机制具有重要意义。在这项研究中，一个新的基于序列的方法来鉴定噬菌体病毒蛋白。在新方法中，蛋白质序列最初由g-gap二肽组合物配制。随后，方差分析（ANOVA）与增量特征选择（IFS）被用来寻找最佳的特征集。据观察，在刀切交叉验证中，包括160个优化特征的最优特征集可以产生85.02%的最大准确率。通过特征分析，我们发现两个氨基酸之间的相关性对噬菌体病毒体蛋白的预测比其他相关性更重要，并且一些1-gap二肽是重要的，主要贡献于病毒体蛋白的预测。这种分析将提供新的见解噬菌体病毒体蛋白的功能。在此基础上，建立了PVPred在线服务器，可从网站（http：//lin.uestc.edu.cn/server/PVPred）免费访问。我们相信，PVPred将成为研究噬菌体病毒体蛋白和指导相关实验验证的有力工具。
The bacteriophage virion proteins play extremely important roles in the fate of host bacterial cells. Accurate identification of bacteriophage virion proteins is very important for understanding their functions and clarifying the lysis mechanism of bacterial cells. In this study, a new sequence-based method was developed to identify phage virion proteins. In the new method, the protein sequences were initially formulated by the g-gap dipeptide compositions. Subsequently, the analysis of variance (ANOVA) with incremental feature selection (IFS) was used to search for the optimal feature set. It was observed that, in jackknife cross-validation, the optimal feature set including 160 optimized features can produce the maximum accuracy of 85.02%. By performing feature analysis, we found that the correlation between two amino acids with one gap was more important than other correlations for phage virion protein prediction and that some of the 1-gap dipeptides were important and mainly contributed to the virion protein prediction. This analysis will provide novel insights into the function of phage virion proteins. On the basis of the proposed method, an online web-server, PVPred, was established and can be freely accessed from the website (http://lin.uestc.edu.cn/server/PVPred). We believe that the PVPred will become a powerful tool to study phage virion proteins and to guide the related experimental validations.