Department of Electronics and Information Engineering, Chonbuk National University, Jeonju 54896, South Korea.
Department of Electronics and Information Engineering, Chonbuk National University, Jeonju 54896, South Korea; Department of Computer Science, Abdul Wali Khan University, Mardan 23200, Pakistan.
Genomics. 2020 Mar;112(2):1396-1403. doi: 10.1016/j.ygeno.2019.08.009. Epub 2019 Aug 19.
The promoter is a regulatory DNA region and important for gene transcriptional regulation. It is located near the transcription start site (TSS) upstream of the corresponding gene. In the post-genomics era, the availability of data makes it possible to build computational models for robustly detecting the promoters as these models are expected to be helpful for academia and drug discovery. Until recently, developed models focused only on discriminating the sequences into promoter and non-promoter. However, promoter predictors can be further improved by considering weak and strong promoter classification. In this work, we introduce a hybrid model, named iPSW(PseDNC-DL), for identification of prokaryotic promoters and their strength. It combines a convolutional neural network with a pseudo-di-nucleotide composition (PseDNC). The proposed model iPSW(PseDNC-DL) has been evaluated on the benchmark datasets and outperformed the current state-of-the-art models in both tasks namely promoter identification and promoter strength identification. The developed tool iPSW(PseDNC-DL) has been constructed in a web server and made freely available at https://home.jbnu.ac.kr/NSCL/PseDNC-DL.htm.
启动子是一个调节 DNA 区域,对于基因转录调控很重要。它位于相应基因转录起始位点(TSS)的上游附近。在后基因组时代,数据的可用性使得构建用于稳健检测启动子的计算模型成为可能,因为这些模型有望对学术界和药物发现有所帮助。直到最近,开发的模型仅专注于将序列区分成启动子和非启动子。然而,通过考虑弱启动子和强启动子分类,可以进一步改进启动子预测器。在这项工作中,我们引入了一种名为 iPSW(PseDNC-DL)的混合模型,用于识别原核启动子及其强度。它将卷积神经网络与伪二核苷酸组成(PseDNC)相结合。在所评估的基准数据集上,所提出的 iPSW(PseDNC-DL)模型在启动子识别和启动子强度识别这两个任务上均优于当前最先进的模型。所开发的 iPSW(PseDNC-DL)工具已在网络服务器上构建,并可在 https://home.jbnu.ac.kr/NSCL/PseDNC-DL.htm 上免费获得。