SecAlignVisualizer

SecAlignVisualizer is a tool for visualizing multiple sequence alignments with secondary structure annotations. It parses .PDB files to extract helix and sheet information, maps this information to sequence alignments, and generates an .HTML representation with color-coded secondary structures.

Features

• Parse PDB files to extract helix and sheet secondary structure information.
• Map secondary structure information to sequence alignments.
• Generate HTML representations of sequence alignments with color-coded secondary structures.

What you need to run

• .PDB files where each one contain the helix and sheet secondary structure information.
• .fas or .aln file that contain the multi-sequence alignment file

Installation

Ensure you have Python and the required libraries installed:

pip install biopython

Usage

1. Prepare .PDB Files: Ensure your PDB files are available in the desired directory.

2. Create Alignment: Use your favorite alignment tool (e.g., Clustal Omega, MUSCLE) to generate a multiple sequence alignment file in FASTA format (.fas) or .aln format.

3. Open the Main.ipynb, Update the file path below in the code:

• pdb_files_dir = "Replace_with_FOLDER_path"
• alignment_file = "Replace_with_path_to_alignment_file"

4. Run the final block and open Output.html

Contributing

Contributions are welcome! Please fork the repository and submit a pull request for review.