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.

References in zbMATH (referenced in 27 articles )

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  1. Clote, Peter; Bayegan, Amir H.: RNA folding kinetics using Monte Carlo and Gillespie algorithms (2018)
  2. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  3. Keith, Jonathan M. (ed.): Bioinformatics. Volume II: structure, function, and applications (2017)
  4. Gatter, Thomas; Giegerich, Robert; Saule, Cédric: Integrating Pareto optimization into dynamic programming (2016)
  5. Picardi, Ernesto (ed.): RNA bioinformatics (2015)
  6. Giegerich, Robert; Touzet, H’el’ene: Modeling dynamic programming problems over sequences and trees with inverse coupled rewrite systems (2014)
  7. Kasabov, Nikola (ed.): Springer handbook of bio-/neuro-informatics (2014)
  8. Clote, Peter; Ponty, Yann; Steyaert, Jean-Marc: Expected distance between terminal nucleotides of RNA secondary structures (2012)
  9. Rodríguez-Ezpeleta, Naiara (ed.); Hackenberg, Michael (ed.); Aransay, Ana M. (ed.): Bioinformatics for high throughput sequencing (2012)
  10. Chen, Qingfeng; Li, Gang; Chen, Yi-Ping Phoebe: Interval-based distance function for identifying RNA structure candidates (2011)
  11. Ouangraoua, Aïda; Guignon, Valentin; Hamel, Sylvie; Chauve, Cedric: A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes (2011)
  12. Brabrand, Claus; Giegerich, Robert; Møller, Anders: Analyzing ambiguity of context-free grammars (2010)
  13. 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: updates to the RNA families database (2009) ioport
  14. Kari, Lila; Seki, Shinnosuke: On pseudoknot-bordered words and their properties (2009)
  15. Blackshields, Gordon; Larkin, Mark; Wallace, Iain M.; Wilm, Andreas; Higgins, Desmond G.: Fast embedding methods for clustering tens of thousands of sequences (2008)
  16. Lladser, Manuel E.; Betterton, M. D.; Knight, Rob: Multiple pattern matching: a Markov chain approach (2008)
  17. Machado-Lima, Ariane; del Portillo, Hernando A.; Durham, Alan Mitchell: Computational methods in noncoding RNA research (2008)
  18. Metzler, Dirk; Nebel, Markus E.: Predicting RNA secondary structures with pseudoknots by MCMC sampling (2008)
  19. Ponty, Yann: Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy (2008)
  20. Sato, Kengo; Morita, Kensuke; Sakakibara, Yasubumi: PSSMTS: Position specific scoring matrices on tree structures (2008)

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