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Rfam 15: RNA families database in 2025
Nancy Ontiveros1, Emma Cooke2, Eric P Nawrocki3
1European Molecular Biology Laboratory, Wellcome Genome Campus, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.
Biorxiv : the Preprint Server for Biology
|October 7, 2024
Summary
The Rfam database (release 15.0) significantly expands its non-coding RNA (ncRNA) families and genome coverage. Updates improve RNA structure accuracy and annotation quality for research and machine learning applications.
Area of Science:
- Bioinformatics
- Genomics
- Molecular Biology
Background:
- Rfam is a key database for non-coding RNA (ncRNA) families.
- Accurate ncRNA annotation is crucial for genomic research and functional studies.
Purpose of the Study:
- To detail the significant updates in Rfam release 15.0.
- To highlight improvements in ncRNA family coverage, annotation quality, and data accessibility.
Main Methods:
- Expanded Rfamseq database to include 26,106 genomes.
- Utilized experimentally determined 3D structures and R-scape covariation analysis for structural refinement.
- Updated Gene Ontology and Sequence Ontology annotations.
Main Results:
- Incorporated 76% more genomes, including UniProt reference proteomes and viral genomes.
- Enhanced 65 RNA families with 3D structures and refined 26 families using R-scape.
- Achieved 75% GO term coverage, added 14 new Hepatitis C Virus RNA families, and synchronized 1,603 microRNA families with miRBase.
Conclusions:
- Rfam release 15.0 substantially increases data scope and annotation precision.
- These enhancements bolster Rfam's utility in RNA research, genome annotation, and machine learning model development.
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