Peptoid MSA Viewer

Peptoid MSA Viewer is a Streamlit-based web application designed for visualizing and analyzing Multiple Sequence Alignments (MSA) of peptoids. The tool allows users to input MSA data, apply custom color mappings, and export results for further analysis.

Features

• FASTA Upload & Parsing – Supports input of MSA data in FASTA format.
• Custom Color Mapping – Assign user-defined colors to specific peptoid residues.
• Dynamic Visualization – Automatically adjusts for varying sequence lengths.
• Export Options – Save alignment visualizations as PNG or SVG files.
• User-Friendly Interface – Interactive design built with Streamlit.

Usage

Online Deployment

This application is hosted on Hugging Face Spaces. You can access it directly via the following link:

Peptoid MSA Viewer on Hugging Face Spaces

Local Installation

To run the application locally, follow these steps:

1. Clone the repository:

   git clone <link_to_repo>  
   cd peptoid-msa
   

2. Install dependencies:

   pip install -r requirements.txt
   

3. Start the Streamlit app:

   streamlit run app.py
   

File Formats

• Input: FASTA formatted 3-letter code peptoid sequences pasted into the input box.
• Output: PNG, SVG, or FASTA download.

Dependencies

The application requires the following Python packages:

• numpy
• plotly
• streamlit
• kaleido

All dependencies are listed in requirements.txt and will be installed automatically.

Author

Allon Goldberg
Research Assistant
Flatiron Institute, Center for Computational Biology (CCB)
Biomolecular Design Group

March 13, 2025

Acknowledgments

If you use this tool in your research, please cite appropriately.