Rfam

Rfam is a comprehensive database of RNA families that provides curated multiple sequence alignments, consensus secondary structures, and covariance models (CMs) used to identify homologous RNA sequences. Each entry corresponds to a RNA family, spanning a range from small noncoding RNAs to larger structural RNA elements. Alignments are built from seed sequences curated by experts and extended through automated searches to capture related sequences.

Entries in Rfam include an accession (for example RFxxxxx), a descriptive text, taxonomic distribution, a curated seed alignment, a full alignment, and a covariance model. The conserved secondary structure is represented for each family and is incorporated into the CM to capture both sequence and structural conservation. The models enable sensitive homology searches in genomic and transcriptomic data using the Infernal software.

Access and use: The database is available online at rfam.org, offering web search and browsing interfaces as well as downloadable data. Data formats include Stockholm alignments and Infernal CM model files. Rfam data are widely used in genome annotation pipelines, comparative genomics, and studies of RNA evolution and structure.

Origin and scope: Rfam is a community-resource that aggregates RNA family information through manual curation and computational methods, incorporating new evidence from the literature and published sequence data. It complements other RNA resources and serves as a foundational reference for RNA annotation, discovery, and structural analysis in diverse organisms.