Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.
Nucleic Acids Res. 2024 Jul 5;52(W1):W7-W12. doi: 10.1093/nar/gkae433.
Sequence-dependent DNA shape plays an important role in understanding protein-DNA binding mechanisms. High-throughput prediction of DNA shape features has become a valuable tool in the field of protein-DNA recognition, transcription factor-DNA binding specificity, and gene regulation. However, our widely used webserver, DNAshape, relies on statistically summarized pentamer query tables to query DNA shape features. These query tables do not consider flanking regions longer than two base pairs, and acquiring a query table for hexamers or higher-order k-mers is currently still unrealistic due to limitations in achieving sufficient statistical coverage in molecular simulations or structural biology experiments. A recent deep-learning method, Deep DNAshape, can predict DNA shape features at the core of a DNA fragment considering flanking regions of up to seven base pairs, trained on limited simulation data. However, Deep DNAshape is rather complicated to install, and it must run locally compared to the pentamer-based DNAshape webserver, creating a barrier for users. Here, we present the Deep DNAshape webserver, which has the benefits of both methods while being accurate, fast, and accessible to all users. Additional improvements of the webserver include the detection of user input in real time, the ability of interactive visualization tools and different modes of analyses. URL: https://deepdnashape.usc.edu.
序列相关的 DNA 构象在理解蛋白质-DNA 结合机制方面起着重要作用。高通量预测 DNA 形状特征已成为蛋白质-DNA 识别、转录因子-DNA 结合特异性和基因调控领域的一种有价值的工具。然而,我们广泛使用的 web 服务器 DNAshape 依赖于统计汇总的五聚体查询表来查询 DNA 形状特征。这些查询表不考虑长于两个碱基对的侧翼区域,并且由于在分子模拟或结构生物学实验中实现足够的统计覆盖存在限制,目前获取六聚体或更高阶 k- 聚体的查询表仍然不切实际。最近的一种深度学习方法 Deep DNAshape 可以预测考虑到长达七个碱基对侧翼区域的 DNA 片段核心的 DNA 形状特征,该方法在有限的模拟数据上进行训练。然而,Deep DNAshape 安装起来相当复杂,与基于五聚体的 DNAshape web 服务器相比,它必须在本地运行,这给用户造成了障碍。在这里,我们提出了 Deep DNAshape web 服务器,它结合了这两种方法的优点,同时具有准确性、速度和对所有用户的可访问性。该服务器的其他改进包括实时检测用户输入、交互式可视化工具的功能以及不同分析模式的能力。网址:https://deepdnashape.usc.edu.