This project analyzes the genetic differences between the SARS-CoV-2 Delta and Omicron variants. Using sequence alignment, phylogenetic tree construction, and mutation analysis, we identify key variations that impact the virus’s transmissibility and mutation resistance.
- Consensus Sequence Construction: Generates a representative consensus sequence from multiple reference sequences by selecting the most common residues at each position.
- Multiple Sequence Alignment: Aligns genetic sequences to identify conserved and mutated regions.
- Phylogenetic Tree Construction: Visualizes evolutionary relationships using the Neighbor-Joining algorithm.
- Mutation Analysis: Computes nucleotide composition percentages and CG content to assess mutation resistance.
- Mismatch Identification: Detects positions and lengths of consecutive mismatches between variants and identifies variant-specific mutations based on frequency across case sequences.
- Data Visualization: Provides graphical representation of mutation density and sequence similarities.
- Python (for data processing and sequence analysis)
- Biopython (for sequence alignment and phylogenetic tree generation)
- Matplotlib (for data visualization)
- ClustalW (for multiple sequence alignment)
- Generated phylogenetic tree showing the evolutionary relationship between the variants.
- Identified key mutation regions and classified them based on their impact.
- Visualized nucleotide composition differences between Delta and Omicron.
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