iPSW(2L)-PseKNC: A two-layer predictor for identifying promoters and their strength by hybrid features via pseudo K-tuple nucleotide composition
iPSW(2L)-PseKNC: A two-layer predictor for identifying promoters and their strength by hybrid features via pseudo K-tuple nucleotide composition
复制标题
iPSW(2L)-PseKNC：一种两层预测器，用于通过伪 K 元组核苷酸组成的杂交特征来识别启动子及其强度
DOI：
10.1016/j.ygeno.2018.12.001
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发表时间：
2019
期刊：
影响因子：
4.4
通讯作者：
Chou Kuo Chen
中科院分区：
文献类型：
--
作者：
Xiao Xuan;Xu Zhao Chun;Qiu Wang Ren;Wang Peng;Ge Hui Ting;Chou Kuo Chen
启动子是约81-1000个碱基对长的调节DNA区域，通常位于给定基因沿着上游的转录起始位点（TSS）附近。启动子通过与转录因子结合，为基因转录调控提供了起点，在基因转录调控中起着至关重要的作用。随着后基因组时代DNA序列的爆炸式增长，开发有效识别启动子的计算方法已成为一个紧迫的挑战，因为由此获得的信息对于基础研究和药物开发都非常有用。虽然在这方面开发了一些预测方法，但大多数方法仅限于鉴定查询DNA序列是否为启动子。然而，根据启动子在转录激活和表达水平上的强弱不同，可将启动子分为强启动子和弱启动子两类。本文将核苷酸的物理化学性质和核苷酸密度融合到PseKNC（pseudo K-tuple nucleotide composition）中，提出了一种新的双层预测模型iPSW（2L）-PseKNC。第一层用于预测查询DNA序列样本是否具有启动子，第二层用于预测启动子的强度。通过严格的交叉验证已经观察到，第一层子预测器在识别启动子和非启动子方面明显上级现有的最先进的预测器，并且第二层子预测器可以做现有预测器无法做到的事情。此外，iPSW（2L）-PseKNC的网络服务器已经建立在http：//www.jci-bioinfo.cn/iPSW（2L）-PseKNC上，广大实验科学家可以很容易地获得他们需要的结果。
The promoter is a regulatory DNA region about 81–1000 base pairs long, usually located near the transcription start site (TSS) along upstream of a given gene. By combining a certain protein called transcription factor, the promoter provides the starting point for regulated gene transcription, and hence plays a vitally important role in gene transcriptional regulation. With explosive growth of DNA sequences in the post-genomic age, it has become an urgent challenge to develop computational method for effectively identifying promoters because the information thus obtained is very useful for both basic research and drug development. Although some prediction methods were developed in this regard, most of them were limited at merely identifying whether a query DNA sequence being of a promoter or not. However, based on their strength-distinct levels for transcriptional activation and expression, promoter should be divided into two categories: strong and weak types. Here a new two-layer predictor, called “iPSW(2L)-PseKNC”, was developed by fusing the physicochemical properties of nucleotides and their nucleotide density into PseKNC (pseudo K-tuple nucleotide composition). Its 1st-layer serves to predict whether a query DNA sequence sample is of promoter or not, while its 2nd-layer is able to predict the strength of promoters. It has been observed through rigorous cross-validations that the 1st-layer sub-predictor is remarkably superior to the existing state-of-the-art predictors in identifying the promoters and non-promoters, and that the 2nd-layer sub-predictor can do what is beyond the reach of the existing predictors. Moreover, the web-server for iPSW(2L)-PseKNC has been established at http://www.jci-bioinfo.cn/iPSW(2L)-PseKNC, by which the majority of experimental scientists can easily get the results they need.