Biopython Tools - Clean & Simple

This repository contains a collection of Biopython-based tools and tutorials for handling various bioinformatics tasks, such as sequence manipulation, alignment, and structure analysis. The repository has been cleaned up and enhanced while keeping the original simplicity.

Project Structure

• data/: Contains example datasets like FASTA files (e.g., chimpanzee mRNA).
• notebooks/: Jupyter Notebooks for demonstrating projects and including examples.
• Tools & Examples/: Your original bioinformatics tools and projects (chimpanzee, databases, etc.).
• projects/: Simple notebook versions of your original projects (5 projects).

Original Projects (Preserved as Tutorials)

1. Chimpanzee mRNA GC Content Analysis:

• Retrieve chimpanzee mRNA sequences using Entrez.
• Perform GC content analysis on the large mRNA dataset.
• Simple visualization and analysis tools.

2. Nucleotide Search and Retrieval:

• Use Entrez to search and retrieve specific nucleotide sequences from databases like NCBI.
• Using other Databases like Expassy and Swissprot.
• Simple cross-database search capabilities.

3. Protein Structure Analysis:

• Fetch protein structures from the Protein Data Bank (PDB).
• Perform structure analysis and visualization using Biopython tools.
• Basic structural analysis features.

4. Pairwise Sequence Alignment:

• Perform global and local sequence alignments to analyze sequence similarity.
• Example alignment of nucleotide sequences (chimpanzee mRNA vs. human mRNA).
• Simple alignment visualization.

Simple Python Projects

1. Chimpanzee mRNA GC Content Analysis (projects/01_chimpanzee_mrna_gc_analysis.py)

• Simple NCBI search for chimpanzee mRNA
• Basic GC content analysis
• Cisualization

2. Nucleotide Search and Retrieval (projects/02_nucleotide_search_retrieval.py)

• Simple Entrez database search
• Basic sequence retrieval
• FASTA export

3. Protein Structure Analysis (projects/03_protein_structure_analysis.py)

• Simple PDB structure download
• Basic structure analysis
• Visualization

4. Pairwise Sequence Alignment (projects/04_pairwise_sequence_alignment.py)

• Simple global and local alignment
• Similarity calculations
• Matrix visualization

5. Metagenomics Analysis (projects/05_metagenomics_analysis.py)

• Simple quality control
• Basic GC content analysis
• Simple classification

Requirements

To install the required Python packages, run:

pip install -r requirements.txt

Quick Start

# Clone the repository
git clone https://github.com/yourusername/Bio-Python.git
cd Bio-Python

# Install dependencies
pip install -r requirements.txt

# Launch Jupyter Lab
jupyter lab

Usage Examples

Your Original Tutorials

# Use your existing notebooks in Tools & Examples/
# They work exactly as before, just cleaner

Simple Python Projects

# Run any Python script in projects/ directory
# Each script is self-contained and easy to follow
# Based on your original work but simplified

Repository Features

• Keeps It Simple: No complex software architecture
• Python Scripts: Everything in easy-to-understand Python scripts
• Your Original Work: Completely preserved as tutorials
• Simple Projects: 5 clean Python scripts based on your work
• Professional Quality: Well-structured and maintainable

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

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Enhanced with ❤️ while keeping it simple and clean