AMIGOS III data (usage examples and benchmark analysis)

This entry includes all materials used to generate the figures and tables in the AMIGOS III publication (Shine et al., 2022). AMIGOSIII-plugin-code.zip contains the code for the AMIGOS III PyMOL plugin, which can also be found at the following page: https://github.com/pylelab/AMIGOSIII. Files beginning with "4en5" were used to generate Figure 1. This includes the 4en5.pdb file, which was used as an input for the AMIGOS III PyMOL plugin, and the following five output files, which were generated using the AMIGOS III NARama feature: 4en5_eta_theta_plot.png (an eta vs theta plot), 4en5_eta_theta_prime_plot.png (an eta' vs theta' plot), 4en5_nucleic_worm_plot.png (a 3D plot of nucleotide position, eta, and theta), 4en5_eta_theta.csv (a spreadsheet of eta and theta values), and 4en5_eta_theta_prime.csv (a spreadsheet of eta' and theta' values). Files beginning with "7mk1-chainC" were used to generate Figure S2. This includes the 7mk1.pdb file, which was used as an input for the AMIGOS III PyMOL plugin, and the following five output files, which were generated using the AMIGOS III NARama feature: 7mk1-chainC_eta_theta_plot.png (an eta vs theta plot), 7mk1-chainC_eta_theta_prime_plot.png (an eta' vs theta' plot), 7mk1-chainC_nucleic_worm_plot.png (a 3D plot of nucleotide position, eta, and theta), 7mk1-chainC_eta_theta.csv (a spreadsheet of eta and theta values), and 7mk1-chainC_eta_theta_prime.csv (a spreadsheet of eta' and theta' values). The AMIGOSIII-TableS1-FigureS1-ata.xlsx file contains the benchmark data underlying TableS1 and FigureS1, which compares the performance of the motif searching feature of AMIGOS III with the Perl program PRIMOS.

本数据集包含用于生成AMIGOS III学术论文（Shine等人，2022）中所有图表与表格的全部材料。AMIGOSIII-plugin-code.zip包含AMIGOS III PyMOL插件的代码，该代码也可在以下页面获取：https://github.com/pylelab/AMIGOSIII。以“4en5”开头的文件用于生成图1，其中包括作为AMIGOS III PyMOL插件输入的4en5.pdb文件，以及通过AMIGOS III NARama特征生成的五个输出文件：4en5_eta_theta_plot.png（η与θ散点图）、4en5_eta_theta_prime_plot.png（η'与θ'散点图）、4en5_nucleic_worm_plot.png（核苷酸位置、η与θ的三维绘图）、4en5_eta_theta.csv（η与θ值数据表）、4en5_eta_theta_prime.csv（η'与θ'值数据表）。以“7mk1-chainC”开头的文件用于生成补充图S2，其中包括作为AMIGOS III PyMOL插件输入的7mk1.pdb文件，以及通过AMIGOS III NARama特征生成的五个输出文件：7mk1-chainC_eta_theta_plot.png（η与θ散点图）、7mk1-chainC_eta_theta_prime_plot.png（η'与θ'散点图）、7mk1-chainC_nucleic_worm_plot.png（核苷酸位置、η与θ的三维绘图）、7mk1-chainC_eta_theta.csv（η与θ值数据表）、7mk1-chainC_eta_theta_prime.csv（η'与θ'值数据表）。AMIGOSIII-TableS1-FigureS1-ata.xlsx文件包含支撑表S1与图S1的基准数据集，该数据集对比了AMIGOS III的基序搜索功能与Perl程序PRIMOS的性能。