Rfam

The Rfam database can be used for a variety of functions. For each ncRNA family, the interface allows users to: view and download multiple sequence alignments; read annotation; and examine species distribution of family members. There are also links provided to literature references and other RNA databases. Rfam also provides links to Wikipedia so that entries can be created or edited by users. The interface at the Rfam website allows users to search ncRNAs by keyword, family name, or genome as well as to search by ncRNA sequence or EMBL accession number. The database information is also available for download, installation and use using the INFERNAL software package. The INFERNAL package can also be used with Rfam to annotate sequences (including complete genomes) for homologues to known ncRNAs. == Methods ==

In the database, the information of the secondary structure and the primary sequence, represented by the MSA, is combined in statistical models called profile stochastic context-free grammars (SCFGs), also known as covariance models. These are analogous to hidden Markov models used for protein family annotation in the Pfam database. The second MSA is the “full” alignment, and is created as a result of a search using the covariance model against the sequence database. All detected homologs are aligned to the model, giving the automatically produced full alignment. == History ==

Version 1.0 of Rfam was launched in 2003 and contained 25 ncRNA families and annotated about 50 000 ncRNA genes. In 2005, version 6.1 was released and contained 379 families annotating over 280 000 genes. In August 2012, version 11.0 contained 2208 RNA families, while the current version (14.9, released in November 2022) annotates 4108 • 2008 - Rfam: updates to the RNA families database. • 2014 - Rfam 12.0: updates to the RNA families database. • 2020 - Rfam 14: expanded coverage of metagenomic, viral and microRNA families. == Problems ==

• The genomes of higher eukaryotes contain many ncRNA-derived pseudogenes and repeats. Distinguishing these non-functional copies from functional ncRNA is a formidable challenge. • Introns are not modeled by covariance models. ==References==