Rfam: updates to the RNA families database

Gardner, Paul P.; Daub, Jennifer; Tate, John G.; Nawrocki, Eric P.; Kolbe, Diana L.; Lindgreen, Stinus; Wilkinson, Adam C.; Finn, Robert D.; Griffiths-Jones, Sam; Eddy, Sean R.; Bateman, Alex

Rfam is a database of sequence families of structural RNAs, including non-coding RNA genes as well as cisregulatory RNA elements. Rfam release 9.0 contains 603 families, each represented by a multiple sequence alignment of known and predicted representative members of the family, annotated with a consensus base-paired secondary structure. This so-called SEED alignment is used to build a covariance model (CM) with the Infernal software (1) . Each Rfam covariance model is searched against a nucleotide sequence database, producing a list of putative hits. Matches that score above a curated threshold are then aligned to the CM to produce a so-called FULL alignment. This process is outlined diagrammatically in Figure 1 . The Rfam database was developed as a generic approach to the annotation of structured RNA families on genomic sequences (2, 3) , but it has been widely used as a source of reliable alignments and structures for the purposes of training and benchmarking RNA sequence and secondary structure analysis software.