{"prefix":"rfam","name":"Rfam ID","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.","pattern":"^RF\\d{5}$","uri_format":"https://rfam.org/family/$1","providers":[],"homepage":"https://rfam.xfam.org/","contact":{"name":"Anton I Petrov","orcid":"0000-0001-7279-2682","email":"apetrov@ebi.ac.uk","github":"AntonPetrov"},"example":"RF00230","example_extras":[],"deprecated":false,"mappings":{"biocontext":"RFAM","edam":"2356","go":"Rfam","integbio":"nbdc00654","miriam":"rfam","n2t":"rfam","ncbi":"RFAM","togoid":"Rfam","wikidata":"P3523"},"synonyms":[],"keywords":["bibliography/documents","classification","rna","sequence","transcript"],"publications":[{"pubmed":"39526405","doi":"10.1093/nar/gkae1023","title":"Rfam 15: RNA families database in 2025","year":2024},{"pubmed":"29112718","doi":"10.1093/nar/gkx1038","pmc":"PMC5753348","title":"Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families","year":2018},{"pubmed":"25392425","doi":"10.1093/nar/gku1063","pmc":"PMC4383904","title":"Rfam 12.0: updates to the RNA families database","year":2014},{"pubmed":"21062808"},{"pubmed":"18953034"},{"pubmed":"18945806"},{"pubmed":"15608160"},{"pubmed":"12520045"}],"appears_in":[],"depends_on":[],"namespace_in_lui":false,"preferred_prefix":"rfam"}