GenomeSolvers

Welcome to GenomeSolvers, a repository dedicated to solving bioinformatics problems and exploring algorithms related to genome analysis and pattern matching. This repository is ideal for students, researchers, and enthusiasts looking to learn or implement solutions for common challenges in computational biology and string algorithms.

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Features

• Algorithms for finding frequent patterns (k-mers) in DNA sequences.
• Implementation of pattern counting and reverse complement generation.
• Solutions for overlapping pattern occurrences.
• Efficient approaches for genome sequence analysis.
• Modular Python scripts with clear documentation.

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Getting Started

Prerequisites

To run the programs in this repository, you will need:

• Python 3.8 or higher
• A code editor or IDE (e.g., VS Code, PyCharm, or Jupyter Notebook)
• Basic understanding of DNA sequences and string manipulation

Installation

1. Clone the repository:

   git clone https://github.com/your-username/GenomeSolvers.git

2. Navigate to the directory:

   cd GenomeSolvers

3. Install required dependencies (if any):

   pip install -r requirements.txt

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How to Use

1. Pattern Counting

Run the pattern_count.py script to count occurrences of a specific pattern in a DNA sequence.

python pattern_count.py

Provide the DNA sequence and pattern when prompted.

2. Finding Most Frequent k-mers

Run the most_frequent_kmers.py script to find the most frequent k-mers in a sequence.

python most_frequent_kmers.py

Set the sequence and k-mer length in the script or as input.

3. Reverse Complement

Use reverse_complement.py to generate the reverse complement of a DNA sequence.

python reverse_complement.py

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Folder Structure

GenomeSolvers/
|-- pattern_count.py           # Script for pattern counting
|-- most_frequent_kmers.py     # Script for finding most frequent k-mers
|-- reverse_complement.py      # Script for generating reverse complements
|-- examples/                  # Example inputs and outputs
|-- tests/                     # Test cases for all scripts
|-- README.md                  # Documentation

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Contributing

Contributions are welcome! To contribute:

1. Fork this repository.
2. Create a new branch for your feature or bug fix.
3. Submit a pull request with a detailed explanation of your changes.

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License

This project is licensed under the MIT License - see the LICENSE file for details.

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Acknowledgments

Special thanks to the computational biology and bioinformatics community for their inspiration and foundational work in genome analysis.

Mubashir Ali - Founder @ Code with Bismillah | Aspiring Bioinformatics & Data Science Professional | Bridging Biology & Data | Researcher | Genomics, Machine Learning, AI | Python, R, Bioinformatics Tools

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Happy coding! If you have any questions, feel free to open an issue or reach out.