RaptGen-UI: an integrated platform for exploring and analyzing the sequence landscape of HT-SELEX experiments

• Published in: Bioinformatics advances Vol. 5; no. 1; p. vbaf120
• Main Authors: Nakano, Ryota, Iwano, Natsuki, Ichinose, Akiko, Hamada, Michiaki
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.01.2025
• Subjects: Application Note
• ISSN: 2635-0041; 2635-0041
• DOI: 10.1093/bioadv/vbaf120

RaptGen-UI provides intuitive graphical user-interface of the system exploring and analyzing the sequence landscape of high-throughput (HT)-SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiments through machine learning-driven visualization with optimization capabilities. This software enables wet-lab researchers to efficiently analyze HT-SELEX dataset and optimize RNA aptamers without requiring extensive computational expertise. The containerized architecture ensures secure local deployment and supports both of high-performance Graphics Processing Unit (GPU) acceleration and CPU-only environments, making it suitable for various research settings. This software is a web-based application running locally on the user's PC. The frontend is constructed using Next.js and Plotly.js with TypeScript, while the backend is developed using FastAPI, Celery, PostgreSQL RDBMS, and Redis with Python. Each module is encapsulated within Docker containers and deployed via Docker Compose. The system supports both CUDA GPU and CPU-only environments. Source code and documentation are freely available at https://github.com/hmdlab/RaptGen-UI.