This script identifies potential transmembrane regions in protein sequences based on hydrophobicity values. It uses a sliding window approach to calculate the mean and median hydrophobicity of amino acid segments and flags regions that meet specified thresholds.
Note: This script was developed as part of a course project for the "Introduction to Programming" course in the Master's program in Applied Bioinformatics and Data Analysis. It is not an official tool.
- Hydrophobicity Calculation: Computes the mean and median hydrophobicity for each segment of the sequence.
- Threshold-Based Detection: Identifies segments that exceed the specified mean and median hydrophobicity thresholds.
- Customizable Parameters: Allows adjustment of window size and hydrophobicity thresholds.
- Input Sequence: Provide the protein sequence as input.
- Run the Script: Execute the script to find potential transmembrane regions.
window_size: The size of the sliding window (default: 25).threshold_mean: The mean hydrophobicity threshold (default: 0.65).threshold_median: The median hydrophobicity threshold (default: 0.75).
A test sequence file named modified.seq is included in the repository to help you verify the functionality of the script. You can use this sequence to see how the script identifies potential transmembrane regions.
No special installation is required. Just ensure you have Python installed along with the statistics module.