Analysis of the distribution of CpG sites across the genomes of two Bat SARS-like coronaviruses, ZXC21 and ZC45 (2015-2017), using a sliding window approach.

This project analyzes the distribution of CpG sites across the genomes of two Bat SARS-like coronaviruses, ZXC21 and ZC45 (2015-2017), using a sliding window approach. Key findings include:<br>- CpG Counts : Both viruses exhibit regions with elevated CpG densities, suggesting potential functional significance.- Observed/Expected Ratios : Most regions show CpG depletion (O/E ratio &lt; 1), consistent with evolutionary pressures observed in coronaviruses.- Comparison : The results for ZXC21 and ZC45 are nearly identical, indicating similar CpG dynamics and evolutionary strategies.<br> Dataset Includes:- Tab-delimited files (`ZXC21_sliding_window_cpg_analysis.txt`, `ZC45_sliding_window_cpg_analysis.txt`) containing CpG counts and O/E ratios for each sliding window.- Visualizations: - Bar charts showing CpG counts across sliding windows for both viruses. - Line plots illustrating observed/expected (O/E) ratios for both viruses.- Python scripts used for performing the sliding window analysis and generating plots.- Input genome files (`MG772933.gb`, `MG772934.gb`).<br> Methods:The analysis was performed using the following steps:1. Divided the genomes into fixed-size windows (100 bp) with a step size of 50 bp.2. Calculated CpG counts and observed/expected (O/E) ratios for each window.3. Generated visualizations using Python libraries like Pandas and Matplotlib.<br> Implications:This work contributes to understanding the genomic architecture of Bat SARS-like coronaviruses and their evolutionary strategies. The findings align with broader trends observed in coronaviruses, highlighting shared mechanisms of CpG dynamics.<br>Published on Figshare: 10.6084/m9.figshare.28705895

本项目采用滑动窗口分析法（sliding window approach），对2015-2017年采集的两株蝙蝠源SARS样冠状病毒ZXC21与ZC45的基因组中CpG位点（CpG sites）的分布特征展开分析。主要研究结果如下：
- CpG计数：两株病毒均存在CpG密度升高的区域，提示其可能具备潜在功能意义。
- 观测/预期比值（Observed/Expected Ratios，下文简称O/E比值）：绝大多数区域呈现CpG缺失现象（O/E比值＜1），这与冠状病毒所受的进化选择压力相符。
- 对比分析：ZXC21与ZC45的分析结果几乎一致，表明二者具有相似的CpG动态变化模式与进化策略。

本数据集包含以下内容：
- 制表符分隔文本文件（Tab-delimited files）：`ZXC21_sliding_window_cpg_analysis.txt`、`ZC45_sliding_window_cpg_analysis.txt`，存储各滑动窗口的CpG计数与O/E比值数据。
- 可视化结果：
- 柱状图（bar charts）：展示两株病毒各滑动窗口的CpG计数；
- 折线图（line plots）：呈现两株病毒的观测/预期（O/E）比值变化情况。
- Python脚本（Python scripts）：用于执行滑动窗口分析与绘图的代码文件。
- 输入基因组文件（genome files）：`MG772933.gb`、`MG772934.gb`。

本分析采用以下步骤完成：
1. 将基因组划分为固定长度（100 bp）的窗口，步长设置为50 bp。
2. 计算每个窗口的CpG计数与观测/预期（O/E）比值。
3. 借助Pandas、Matplotlib等Python库生成可视化图表。

本研究有助于加深对蝙蝠源SARS样冠状病毒基因组结构及其进化策略的理解。研究结果与冠状病毒领域已报道的整体趋势相符，揭示了CpG动态变化的共通机制。

本数据集已发布于Figshare：10.6084/m9.figshare.28705895