Viral non-coding RNA structure annotation and API-based data retrieval with Rfam and R2DT

作者：Philippa Muston, Sandra Triebel, Eric Nawrocki, Nancy Ontiveros‐Palacios, Isaac Jandalala, Blake Sweeney, Alex Bateman, Manja Marz, Anton I. Petrov, Pedro Madrigal · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2026 · DOI：10.64898/2026.05.10.724034 · 研究领域：RNA and protein synthesis mechanisms、RNA modifications and cancer、Genomics and Phylogenetic Studies

Rfam is a comprehensive database of non-coding RNA (ncRNA) families providing curated sequence alignments, consensus secondary structures, and covariance models for thousands of RNA families. The database is essential for identifying structured non-coding RNAs in newly sequenced genomes and understanding RNA structure-function relationships. Here we present computational protocols for automated ncRNA annotation of viral genomes, and for programmatic interaction with Rfam through its RESTful API. We showcase genome-wide RNA structure visualization from a genome sequence and from a multiple sequence alignment by generating comprehensive 2D structure diagrams using newly developed features in R2DT. We also present practical examples for retrieving family metadata, downloading alignments, accessing secondary structures, and searching user sequences from the Rfam API. These methods enable researchers in virology and RNA biology to integrate Rfam data into custom bioinformatics pipelines, comparative analyses, and machine learning workflows.