Citing Rfam

Rfam makes use of a large amount of publicly available data, especially published multiple sequence alignments and secondary structures, and repackages these data in a single searchable and sustainable resource. We have made every effort to credit individual sources on family pages. If you find any of the data presented here useful, please be sure to credit the primary source as well.

Rfam references

Rfam 15: RNA families database in 2025: Nancy Ontiveros-Palacios, Emma Cooke, Eric P Nawrocki, Sandra Triebel, Manja Marz, Elena Rivas, Sam Griffiths-Jones, Anton I Petrov, Alex Bateman, and Blake Sweeney

Nucleic Acids Research (2024) doi: 10.1093/nar/gkae1023
Rfam 14: expanded coverage of metagenomic, viral and microRNA families: I. Kalvari, E.P. Nawrocki, N. Ontiveros-Palacios, J. Argasinska, K. Lamkiewicz, M. Marz, S. Griffiths-Jones, C. Toffano-Nioche, D. Gautheret, Z. Weinberg, E. Rivas, S.R. Eddy, R.D. Finn, A. Bateman, and A.I. Petrov

Nucleic Acids Research (2020) doi: 10.1093/nar/gkaa1047
Non‐coding RNA analysis using the Rfam database: I. Kalvari, E.P. Nawrocki, J. Argasinska, N. Quinones‐Olvera, R.D. Finn, A. Bateman, and A.I. Petrov

Current Protocols in Bioinformatics (2018) e51. doi: 10.1002/cpbi.51
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families: I. Kalvari, J. Argasinska, N. Quinones-Olvera, E.P. Nawrocki, E. Rivas, S.R. Eddy, A. Bateman, R.D. Finn, and A.I. Petrov

Nucleic Acids Research (2017) doi: 10.1093/nar/gkx1038
Rfam 12.0: updates to the RNA families database: E.P. Nawrocki, S.W. Burge, A. Bateman, J. Daub, R.Y. Eberhardt, S.R. Eddy, E.W. Floden, P.P. Gardner, T.A. Jones, J.T. and R.D. Finn

Nucleic Acids Research (2014) doi: 10.1093/nar/gku1063
Rfam 11.0: 10 years of RNA families: S.W. Burge, J. Daub, R. Eberhardt, J. Tate, L. Barquist, E.P. Nawrocki, S.R. Eddy, P.P. Gardner, and A. Bateman.

Nucleic Acids Research (2012) doi: 10.1093/nar/gks1005
Rfam: Wikipedia, clans and the “decimal” release: P.P. Gardner, J. Daub, J. Tate, B.L. Moore, I.H. Osuch, S. Griffiths-Jones, R.D. Finn, E.P. Nawrocki, D.L. Kolbe, S.R. Eddy, and A. Bateman.

Nucleic Acids Research (2011) doi: 10.1093/nar/gkq1129
Rfam: updates to the RNA families database: P.P. Gardner, J. Daub, J.G. Tate, E.P. Nawrocki, D.L. Kolbe, S. Lindgreen, A.C. Wilkinson, R.D. Finn, S. Griffiths-Jones, S.R. Eddy, and A. Bateman

Nucleic Acids Research (2009) Database Issue 37:D136-D140
The RNA WikiProject: community annotation of RNA families: J. Daub, P.P. Gardner, J. Tate, D. Ramsköld, M. Manske, W.G. Scott, Z. Weinberg, S. Griffiths-Jones, and A. Bateman

RNA (2008) 12:2462-2464
Rfam: annotating non-coding RNAs in complete genomes: S. Griffiths-Jones, S. Moxon, M. Marshall, A. Khanna, S.R. Eddy, A. Bateman

Nucleic Acids Research (2005) Database Issue 33:D121-D124
Rfam: an RNA family database: S. Griffiths-Jones, A. Bateman, M. Marshall, A. Khanna, and S.R. Eddy

Nucleic Acids Research (2003) 31(1):p439-441

Other contributions

Viral non-coding RNA structure annotation and API-based data retrieval with Rfam and R2DT: P. Muston, S. Triebel, et al.

bioRxiv (2026) doi: 10.64898/2026.05.10.724034
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research: F. Hufsky et al.

Briefings in Bioinformatics (2020) doi: 10.1093/bib/bbaa232

Covariance models and stochastic context-free grammars

Annotating functional RNAs in genomes using Infernal: E.P. Nawrocki

Methods in Molecular Biology (2014) 1097:163-97
Infernal 1.1: 100-fold Faster RNA Homology Searches: E. P. Nawrocki, S. R. Eddy

Bioinformatics (2013) 29:2933-2935
Computational Identification of Functional RNA Homologs in Metagenomic Data: E. P. Nawrocki, S. R. Eddy

RNA Biology (2013) 10:1170-1179
Infernal 1.0: Inference of RNA Alignments: E.P. Nawrocki, D.L. Kolbe, S.R. Eddy

Bioinformatics (2009) Mar 23. [Epub ahead of print]
Local RNA Structure Alignment With Incomplete Sequence: D.L. Kolbe, S.R. Eddy

Bioinformatics (2009) Mar 20. [Epub ahead of print]
Query-dependent banding (QDB) for faster RNA similarity searches: E.P. Nawrocki, S.R. Eddy

PLoS Computational Biology (2007) 3(3):e56
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure: S.R. Eddy

BMC Bioinformatics (2002) 2(3):18
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids: R. Durbin, S.R. Eddy, A. Krogh, G. Mitchison

Cambridge University Press (1999) ISBN 0-5216-2971-3
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence: T.M. Lowe, S.R. Eddy

Nucleic Acids Research (1997) 25(5):955-964
RNA sequence analysis using covariance models: S.R. Eddy, R. Durbin

Nucleic Acids Research (1994) 22(11):2079-88