ViroidDB

ViroidDB provides a centralized repository of approximately 10,000 viroid and viroid-like circular RNA sequences and associated annotations to support analysis of their sequences, secondary structures, ribozymes, and classification.

Key Features:

• Database content: Contains ~10,000 unique sequences including viroids, retroviroid-like elements, small circular satellite RNAs, ribozyviruses, and retrozymes.
• Custom circular-RNA pipeline: A pipeline optimized for the unique characteristics of circular RNAs drives per-sequence analyses.
• Secondary structure prediction: Predicts secondary structures for individual circular RNA sequences.
• Ribozyme content annotation: Predicts and annotates ribozyme elements within sequences.
• Cluster membership assignment: Assigns sequences to clusters to support classification and comparative analyses.
• Multiple sequence alignment: Performs multiple sequence alignments for comparative sequence analysis.
• Metadata search and browsing: Supports browsing by sequence type or taxon and typo-tolerant searches of metadata fields.

Scientific Applications:

• Viroid genomics and classification: Comparative genomics and classification of viroids and related circular RNAs.
• Ribozyme discovery and functional annotation: Identification and annotation of ribozyme motifs within circular RNAs.
• Secondary structure and folding studies: Analyses of predicted secondary structures to investigate folding and structural motifs.
• Evolutionary and phylogenetic analyses: Phylogenetic and evolutionary studies of viroids, retroviroid-like elements, ribozyviruses, and retrozymes.
• Plant pathology and host–pathogen research: Studies of viroid-associated disease mechanisms and host interactions.

Methodology:

A custom pipeline predicts each sequence's secondary structure, ribozyme content, and cluster membership and is optimized for circular RNAs.