iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators
iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators
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iTerm-PseKNC：基于序列的预测细菌转录终止子的工具
DOI：
10.1093/bioinformatics/bty827
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发表时间：
2019-05-01
期刊：
影响因子：
5.8
通讯作者：
Lin, Hao
中科院分区：
文献类型：
--
作者：
Feng, Chao-Qin;Zhang, Zhao-Yue;Lin, Hao
动机
转录终止是基因表达的重要调控步骤。如果基因中没有终止子，转录就不能停止，从而导致基因表达异常。检测这种终止子可以确定细菌生物体中的操纵子结构并改善基因组注释。因此，准确鉴定转录终止子在转录调控研究中是必不可少的，也是极其重要的。
结果
在这项研究中，我们开发了一个新的预测称为'iTerm-PseKNC'基于支持向量机识别转录终止子。采用二项分布的方法从伪k元组核苷酸组成（PseKNC）中挑选出最佳特征子集。5折交叉验证测试结果表明，我们提出的方法达到了95%的准确率。为了进一步评估“iTerm-PseKNC”的泛化能力，在实验证实的大肠杆菌和枯草芽孢杆菌基因组中的Rho独立终止子的独立数据集上检查了该模型。因此，E.大肠杆菌和B中终止子的比例为87.5%。枯草芽孢杆菌，正确地鉴定，这表明所提出的模型可以成为一个强大的工具，细菌终止子识别。
可用性和执行
为了方便广大的湿法实验研究者，我们在http：//lin-group.cn/server/iTerm-PseKNC/上建立了“iTerm-PseKNC”的网络服务器，用户可以很容易地获得他们想要的结果，而不需要经过详细的数学方程。
MOTIVATION
Transcription termination is an important regulatory step of gene expression. If there is no terminator in gene, transcription could not stop, which will result in abnormal gene expression. Detecting such terminators can determine the operon structure in bacterial organisms and improve genome annotation. Thus, accurate identification of transcriptional terminators is essential and extremely important in the research of transcription regulations.
RESULTS
In this study, we developed a new predictor called 'iTerm-PseKNC' based on support vector machine to identify transcription terminators. The binomial distribution approach was used to pick out the optimal feature subset derived from pseudo k-tuple nucleotide composition (PseKNC). The 5-fold cross-validation test results showed that our proposed method achieved an accuracy of 95%. To further evaluate the generalization ability of 'iTerm-PseKNC', the model was examined on independent datasets which are experimentally confirmed Rho-independent terminators in Escherichia coli and Bacillus subtilis genomes. As a result, all the terminators in E. coli and 87.5% of the terminators in B. subtilis were correctly identified, suggesting that the proposed model could become a powerful tool for bacterial terminator recognition.
AVAILABILITY AND IMPLEMENTATION
For the convenience of most of wet-experimental researchers, the web-server for 'iTerm-PseKNC' was established at http://lin-group.cn/server/iTerm-PseKNC/, by which users can easily obtain their desired result without the need to go through the detailed mathematical equations involved.