RNAglib: A Python Package for RNA 2.5D Graphs

TL;DR

RNAglib is a Python library that simplifies encoding RNA 3D structures as multi-relational graphs, facilitating machine learning and graph-based analysis of RNA architectures.

Contribution

It provides a comprehensive toolkit for representing RNA 3D structures as 2.5D graphs, including data, visualization, and baseline models, streamlining RNA structure analysis.

Findings

Enables efficient encoding of RNA 3D structures as graphs

Provides tools for visualization and comparison of RNA graphs

Includes baseline performance benchmarks for RNA applications

Abstract

RNA 3D architectures are stabilized by sophisticated networks of (non-canonical) base pair interactions, which can be conveniently encoded as multi-relational graphs and efficiently exploited by graph theoretical approaches and recent progresses in machine learning techniques. RNAglib is a library that eases the use of this representation, by providing clean data, methods to load it in machine learning pipelines and graph-based deep learning models suited for this representation. RNAglib also offers other utilities to model RNA with 2.5D graphs, such as drawing tools, comparison functions or baseline performances on RNA applications. The method and data is distributed as a fully documented pip package. Availability: https://rnaglib.cs.mcgill.ca