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ViroidDB: a database of viroids and viroid-like circular RNAs
Benjamin D Lee1,2, Uri Neri3, Caleb J Oh4
1National Center for Biotechnology Information, National Library of Medicine, National Institutes Health, Bethesda, MD 20894, USA.
Nucleic Acids Research
|November 9, 2021
Summary
ViroidDB is a new database consolidating over 10,000 circular RNA sequences, including viroids and related elements. It offers tools for exploring RNA structures, functions, and evolutionary relationships.
Area of Science:
- Virology
- Bioinformatics
- Genomics
Background:
- Viroids and viroid-like circular RNAs are diverse genetic entities with significant biological impact.
- A centralized, comprehensive resource for these molecules has been lacking.
Purpose of the Study:
- To create ViroidDB, a value-added database for all known viroid and viroid-like circular RNA sequences.
- To provide tools for analyzing secondary structure, ribozyme content, and sequence relationships.
Main Methods:
- Collected approximately 10,000 unique circular RNA sequences, including viroids, retroviroid-like elements, satellite RNAs, ribozyviruses, and retrozymes.
- Developed a custom bioinformatics pipeline for predicting secondary structure, ribozyme activity, and cluster membership.
- Implemented a user-friendly interface with visualizations, multiple sequence alignments, and bulk data download options.
Main Results:
- ViroidDB integrates diverse circular RNA types into a single, searchable resource.
- Predicted secondary structures, ribozyme content, and cluster memberships for all sequences.
- Enabled browsing by sequence type, taxon, and typo-tolerant metadata search.
Conclusions:
- ViroidDB serves as a valuable resource for researchers studying viroids and related circular RNAs.
- The database facilitates exploration of sequence diversity, structural features, and potential functions.
- Provides a foundation for future research into the evolution and impact of these unique RNA molecules.
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