COVID-19 Genome Analysis using Biopython

This project demonstrates how to fetch, analyze, and manipulate the COVID-19 genome using Biopython.

Overview

• Fetches the complete SARS-CoV-2 genome from the NCBI database.
• Analyzes nucleotide sequences (length, composition, etc.).
• Uses Biopython modules: Entrez (for data retrieval) and SeqIO (for parsing sequences).

Dataset

• Accession ID: MN908947.3
• Source: NCBI Nucleotide Database
• Description: Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome.

Code Explanation

1. Fetching the Genome from NCBI

from Bio import Entrez, SeqIO
Entrez.email = "your_email@example.com"  # Required by NCBI

handle = Entrez.efetch(db="nucleotide", id="MN908947", rettype="gb", retmode="text")
recs = list(SeqIO.parse(handle, 'gb'))
handle.close()

• Entrez.efetch(): Fetches genome data from NCBI.
• rettype="gb": Retrieves data in GenBank format.
• SeqIO.parse(): Parses the GenBank record into a sequence object.

2. Extracting the Genome Sequence

covid_dna = recs[0].seq
print(f"Length of the genome: {len(covid_dna)}")

• Extracts the genome sequence as a Seq object.
• Prints the number of nucleotides.

3. Analyzing the Genome

You can perform:

• Length analysis (number of nucleotides).
• Base composition: count of A, T, G, C.
• Sub-sequence extraction for specific regions.

Example:

from Bio.SeqUtils import gc_fraction
gc_content = gc_fraction(covid_dna) * 100
print(f"GC Content: {gc_content:.2f}%")

4. Possible Further Analyses

• Translate the genome into protein sequences.
• Identify open reading frames (ORFs).
• Perform BLAST analysis to compare with other viral genomes.

Requirements

• Python 3.x
• Biopython (pip install biopython)
• Internet access (to fetch data from NCBI)

How to Run

1. Install dependencies:

pip install biopython

2. Set your email in the Entrez.email field (mandatory for NCBI requests).

3. Run the notebook or script to fetch and analyze the genome.

References

• NCBI GenBank Accession: MN908947.3
• Biopython documentation: https://biopython.org/wiki/Documentation

License

Open-source and free to use for research and educational purposes.