Identification of Phage Virion Proteins by Using the g-gap Tripeptide Composition
Identification of Phage Virion Proteins by Using the g-gap Tripeptide Composition
复制标题
使用g间隙三肽组合物鉴定噬菌体病毒粒子蛋白
DOI：
10.2174/1570178615666180910112813
复制
发表时间：
2019-03
影响因子：
0.8
通讯作者：
Tang Lixia
中科院分区：
文献类型：
--
作者：
Yang Liangwei;Gao Hui;Liu Zhen;Tang Lixia
噬菌体广泛分布在细菌宿主聚集的地方。噬菌体蛋白可分为两大类，即具有不同功能的病毒体蛋白和非病毒体蛋白。在实践中，人们主要利用噬菌体病毒体蛋白来阐明细菌细胞的裂解机制和开发新的抗菌药物。因此，准确鉴定噬菌体病毒体蛋白对于理解噬菌体裂解机制至关重要。虽然一些计算方法已经集中在识别病毒粒子蛋白，结果并不令人满意，这给了更多的改进空间。本研究提出了一种基于g-gap三肽组成的噬菌体病毒蛋白序列鉴定方法。该方法首先从ggap三肽序列中提取蛋白质特征。随后，我们得到了一个最佳的特征子集进行增量特征选择（IFS）的信息增益。最后，使用支持向量机（SVM）作为分类器来区分病毒体蛋白和非病毒体蛋白。在10倍交叉验证测试中，我们提出的方法实现了97.40%的准确性，AUC为0.9958，优于最先进的方法。实验结果表明，该方法在噬菌体病毒蛋白的鉴定中具有良好的应用前景。
Phages are widely distributed in locations populated by bacterial hosts. Phage proteins can be divided into two main categories, that is, virion and non-virion proteins with different functions. In practice, people mainly use phage virion proteins to clarify the lysis mechanism of bacterial cells and develop new antibacterial drugs. Accurate identification of phage virion proteins is therefore essential to understanding the phage lysis mechanism. Although some computational methods have been focused on identifying virion proteins, the result is not satisfying which gives more room for improvement. In this study, a new sequence-based method was proposed to identify phage virion proteins using g-gap tripeptide composition. In this approach, the protein features were firstly extracted from the ggap tripeptide composition. Subsequently, we obtained an optimal feature subset by performing incremental feature selection (IFS) with information gain. Finally, the support vector machine (SVM) was used as the classifier to discriminate virion proteins from non-virion proteins. In 10-fold crossvalidation test, our proposed method achieved an accuracy of 97.40% with AUC of 0.9958, which outperforms state-of-the-art methods. The result reveals that our proposed method could be a promising method in the work of phage virion proteins identification.
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DOI：
10.3390/molecules21010095
发表时间：
2016-01-19
期刊：
Molecules (Basel, Switzerland)
影响因子：
--
作者：
Jia J;Liu Z;Xiao X;Liu B;Chou KC
通讯作者：
Chou KC
影响因子：
14.9
作者：
Chen W;Luo L;Zhang L
通讯作者：
Zhang L
DOI：
10.1016/j.omtn.2018.03.012
发表时间：
2018-06-01
期刊：
Molecular therapy. Nucleic acids
影响因子：
--
作者：
Chen W;Feng P;Yang H;Ding H;Lin H;Chou KC
通讯作者：
Chou KC
DOI：
10.1002/1097-0134(20010101)42:1
发表时间：
2001
期刊：
Proteins: Structure
影响因子：
--
作者：
S. Takada
通讯作者：
S. Takada
影响因子：
5.8
作者：
Chou, KC
通讯作者：
Chou, KC