genomic_analysis.

Genomic Analysis Script

This Python script utilizes the Biopython library to perform various analyses on genomic data retrieved from the National Center for Biotechnology Information (NCBI) using its E-utilities. The script covers tasks such as fetching genomic data, reverse complementing sequences, calculating GC skew, visualizing genomic features, and generating files compatible with the UCSC Genome Browser.

Requirements

• Python 3
• Biopython
• Matplotlib

Setup

1. Install the required libraries:

   pip install biopython matplotlib

2. Update the Entrez.email variable in the script with a valid email address. This is required for using NCBI's E-utilities.

Usage

Replace the placeholder accession number ("JX573431.1") in the script with the actual accession number you want to analyze.

# Replace 'your_accession_number' with the actual accession number you want to analyze
accession_number = "JX573431.1"

Run the script:

python genomic_analysis_script.py

Functionality

1. Fetch Genomic Data

The script fetches genomic data from NCBI using the provided accession number.

2. Reverse Sequences

It reverses the retrieved genomic sequence to its complement.

3. Calculate GC Skew

The script calculates and visualizes the GC skew of the reversed sequence.

4. Annotate Genes

It extracts and prints information about genes, including their locations and descriptions.

5. Extract Gene Sequences

The script extracts gene sequences and stores them for further analysis.

6. Create BED File

It generates a BED file (gene_locations.bed) containing information about gene locations.

7. Create Track File

A track file (trackDb.txt) is created for use with the UCSC Genome Browser, providing a custom track description.

8. Calculate Coverage

The script calculates coverage based on genomic features.

9. Plot Coverage

It generates a coverage plot and saves it to a file.

10. Visualize Gene Locations

The script visualizes gene locations on the genomic sequence and saves the plot to a file.