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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