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Updated: May 26, 2026
06:44
Confocal Imaging of Double-Stranded RNA and Pattern Recognition Receptors in Negative-Sense RNA Virus Infection
Published on: January 26, 2019
Viral non-coding RNA structure annotation and API-based data retrieval with Rfam and R2DT
Philippa Muston1, Sandra Triebel2, Eric Nawrocki3
1European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, United Kingdom.
Biorxiv : the Preprint Server for Biology
|May 25, 2026
Summary
Rfam database now offers automated non-coding RNA (ncRNA) annotation for viral genomes and programmatic access via its RESTful API. This enhances RNA biology research by enabling custom bioinformatics pipelines and machine learning workflows.
Area of Science:
- Bioinformatics
- Computational Biology
- RNA Biology
Background:
- Rfam is a critical database for non-coding RNA (ncRNA) families, offering alignments, structures, and models.
- It aids in identifying structured ncRNAs and understanding RNA structure-function relationships.
Purpose of the Study:
- To present computational protocols for automated ncRNA annotation of viral genomes.
- To enable programmatic interaction with the Rfam database via its RESTful API.
Main Methods:
- Developed computational protocols for automated ncRNA annotation of viral genomes.
- Utilized Rfam's RESTful API for programmatic data retrieval and interaction.
- Employed R2DT for genome-wide RNA structure visualization and 2D diagram generation.
Main Results:
- Demonstrated automated ncRNA annotation for viral genomes.
- Showcased genome-wide RNA structure visualization from sequence and alignments.
- Provided practical examples for accessing Rfam metadata, alignments, and structures via API.
Conclusions:
- The presented methods facilitate the integration of Rfam data into custom bioinformatics pipelines.
- Researchers can now more easily perform comparative analyses and machine learning workflows involving ncRNAs.
- Enhanced tools support virology and RNA biology research through improved data accessibility and analysis capabilities.
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