Biopython Tools

This repository contains a collection of Biopython-based tools and tutorials for handling various bioinformatics tasks, such as sequence manipulation, alignment, and structure analysis.

Project Structure

• data/: Contains example datasets like FASTA files (e.g., chimpanzee mRNA).
• notebooks/: Jupyter Notebooks for demonstrating projects and including examples.
• tools/: Python scripts implementing and tutoring bioinformatics tools using Biopython.

Features

• Sequence Manipulation: Reverse complement, transcription, translation, GC content calculation.
• Sequence Alignment: Global and local alignment for nucleotide and protein sequences.
• Database Retrieval: Fetch sequences from NCBI databases (e.g., chimpanzee mRNA).
• Protein Structure Analysis: Retrieve and analyze protein structures from PDB.
• Sliding Window GC Content: Analyze GC content in sliding windows across large datasets.
• File Format Conversion: FASTA, GenBank, and other bioinformatics formats.

Example Projects

1. Chimpanzee mRNA GC Content Analysis:

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

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.

3. Protein Structure Analysis:

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

4. Pairwise Sequence Alignment:

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

Requirements

To install the required Python packages, run:

pip install -r requirements.txt