This project performs DNA sequence alignment and protein secondary structure prediction. Global and local alignment algorithms are implemented. Chou-Fasman algorithm has been implemented for predicting protein secondary structures based on amino acid sequences.
- Global Sequence Alignment: Aligns two DNA sequences using the Needleman-Wunsch algorithm.
- Local Sequence Alignment: Aligns regions of similarity within two DNA sequences using the Smith-Waterman algorithm.
- Protein Structure Prediction: Predicts secondary structures (alpha helices, beta sheets, and turns) using the Chou-Fasman algorithm.
To get started, clone the repository and ensure you have Python installed:
```bash
git clone https://github.com/your-repo/DNA-Sequence-Alignment-and-Protein-Structure-Prediction.git
cd DNA-Sequence-Alignment-and-Protein-Structure-Prediction
```
Install any necessary Python packages:
```bash pip install -r requirements.txt ```
Note: The `requirements.txt` file should be added with the necessary dependencies.
To perform a global sequence alignment, run the following command:
'bash python GlobalAlignment.py sequence1.txt sequence2.txt '
To perform a local sequence alignment, use:
'bash python LocalAlignment.py sequence1.txt sequence2.txt '
To predict the secondary structure of a protein sequence:
```bash python ChouFasman.py protein_sequence.txt ```
The output will be saved in secondary_structure_output.txt.
The secondary_structure_output.txt file will contain the predicted secondary structure for the input protein sequence, indicating regions of alpha helices, beta sheets, and turns.