Rfam

Rfam provides a curated database of non-coding RNA (ncRNA) families represented by multiple sequence alignments, consensus secondary structures, and covariance models for homology detection and annotation.

Key Features:

• Manually Curated Data: Each RNA family includes manually curated multiple sequence alignments and consensus secondary structures.
• Covariance Models (CMs): Covariance models are provided for sensitive homology detection of ncRNA sequences.
• Infernal 1.1 Integration: The search pipeline uses Infernal 1.1 to perform homology searches.
• Comprehensive Annotations: Annotations include information from Wikipedia, taxonomy, and ontology databases.
• Expanded Family Collection: The release includes 260 new families, including the large subunit ribosomal RNA family.
• Sequence- and Structure-based RNA Motifs: Information on short sequence- and structure-based RNA motifs within families is provided.

Scientific Applications:

• RNA Structure–Function Studies: Analysis of consensus secondary structures and alignments to investigate ncRNA structure–function relationships.
• Genomics and Metagenomics Annotation: Identification and annotation of ncRNA sequences in genomic and metagenomic datasets using covariance models and homology searches.
• Evolutionary Studies: Comparative analysis of RNA families to study evolutionary conservation and divergence across species.

Methodology:

Multiple sequence alignments and consensus secondary structures are used to build covariance models, and homology detection is performed via an Infernal 1.1–based search pipeline.