Rfam search

Rfam search identifies and annotates non-coding RNA (ncRNA) families in genomic and metagenomic datasets using the Rfam database and Infernal 1.1 for homology detection.

Key Features:

• Curated data collection: Rfam provides a curated collection of ncRNA families with multiple sequence alignments, consensus secondary structures, and annotations integrated from Wikipedia, taxonomy, and ontology databases.
• Enhanced search pipeline: Searches use Infernal 1.1 to improve homology detection sensitivity via covariance models (CMs).
• Expanded database content: Rfam 12.0 added 260 RNA families, including the large subunit ribosomal RNA family and newly annotated short sequence- and structure-based RNA motifs.
• Genomic and metagenomic annotation: The search capability supports annotation of ncRNAs in both genomic and metagenomic datasets.

Scientific Applications:

• ncRNA annotation: Annotating non-coding RNAs across organisms in genomic and metagenomic datasets based on sequence and structural models.
• Homology detection and family assignment: Detecting homologous RNA sequences and assigning them to Rfam families using covariance models.
• Functional and evolutionary inference: Inferring functional roles and evolutionary relationships of ncRNAs from family membership, alignments, and consensus secondary structures.

Methodology:

Searches employ Infernal 1.1, which uses covariance models (CMs) constructed from multiple sequence alignments and consensus secondary structures to detect homologous RNA sequences in genomic and metagenomic datasets.