CoV_2_MSA_Protocol

This release introduces a comprehensive protocol for the multiple sequence alignment (MSA) of SARS-CoV-2 sequences. It encompasses the entire workflow from sequence acquisition to the application of multiple alignment techniques. Key highlights include the extraction of over 1.6 million sequences from GISAID, dataset construction for variants of concern, and the innovative approach to overcome GISAID's download limitations. We also detail the process of identifying non-synonymous variations, structural modeling, and the subsequent application in drug repurposing efforts against SARS-CoV-2. This protocol aims to provide researchers with a detailed guide for analyzing the genomic sequences of SARS-CoV-2, including scripts for sequence extraction, MSA processing, consensus sequence identification, and visualization of variations within the Spike protein's receptor-binding domain. Whether you're exploring the impact of mutations on vaccine efficacy or searching for potential therapeutic targets, this release offers valuable tools and insights for your research.