Analysis of Intergenic Regions and CpG Distribution in SARS-CoV-2 (Wuhan-Hu-1 Genome)

<br>This project focuses on the analysis of intergenic regions and CpG distribution in the SARS-CoV-2 genome (Wuhan-Hu-1). The study involves extracting intergenic regions from the GenBank annotation file (<code>wuhan_hu_1.gb</code>), calculating CpG counts and densities, and visualizing the results. Key components of this project include:<b>Python Script (</b><code><strong>process_python.py</strong></code><b>) </b>: A script used to process the GenBank file, identify gaps between annotated features, and calculate CpG metrics (counts and densities) for intergenic regions.<b>Results File (</b><code><strong>intergenic_regions.csv</strong></code><b>) </b>: A CSV file containing detailed results of the analysis, including the length, CpG count, and CpG density (per 100 nucleotides) for each intergenic region.<b>Visualization Plots (</b><code><strong>cpg_counts_plot.png</strong></code><b> and </b><code><strong>cpg_densities_plot.png</strong></code><b>) </b>: Bar charts showing the number of CpG sites and their densities across intergenic regions, providing insights into the sparse distribution of CpG dinucleotides in non-coding regions.<b>Input File (</b><code><strong>wuhan_hu_1.gb</strong></code><b>) </b>: The GenBank file (MN908947.3) containing the annotated genome sequence of SARS-CoV-2, used as input for the analysis.<br>Each part of the study is uploaded as a separate file, and these components will later be combined to produce a comprehensive final article on the genomic characteristics of SARS-CoV-2, particularly focusing on its intergenic regions and CpG suppression mechanisms.<br>