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Rfam 15: RNA families database in 2025
Nancy Ontiveros-Palacios1, Emma Cooke2, Eric P Nawrocki3
1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Nucleic Acids Research
|November 11, 2024
Summary
The Rfam database now includes more genomes and enhanced RNA family annotations. These updates improve RNA research, genome annotation, and machine learning model development.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- The Rfam database is a key resource for non-coding RNA families.
- Accurate RNA family data is crucial for biological research and genome annotation.
Purpose of the Study:
- To detail the significant updates in Rfam release 15.0.
- To highlight improvements in genome coverage, annotation quality, and data accessibility.
Main Methods:
- Expanded Rfamseq database to over 26 million genomes.
- Incorporated 3D structures and R-scape covariation analysis for RNA family refinement.
- Updated Gene Ontology and Sequence Ontology annotations.
Main Results:
- Increased genome coverage by 76% and enhanced 65 RNA families with structural data.
- Improved Gene Ontology term coverage to 75% of families.
- Added 14 new Hepatitis C Virus RNA families and synchronized microRNA families with miRBase.
Conclusions:
- Rfam release 15.0 significantly expands data scope and annotation accuracy.
- Enhanced Rfam supports RNA research, genome annotation, and machine learning applications.
- The updates solidify Rfam's role as an essential resource for the scientific community.
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