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Rfam

swMATH ID: 4637
Software Authors: Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A
Description: The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion. Rfam families are frequently built from external sources, we ask that if you find a particular family useful for your work that you cite both Rfam and the primary source of our data.
Homepage: http://rfam.xfam.org/
Related Software: Infernal; ViennaRNA; R; Rnamotif; KEGG; BLAT; ClustalW; RSEARCH; Cd-hit; CONTRAfold; Bioconductor; Rnaz; MAFFT; edgeR; UniProt; T-coffee; VARNA; Mfold; RNAshapes; MARNA
Cited in: 25 Documents

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