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 also be sure to credit the primary source also.
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 SweeneyNucleic 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. PetrovNucleic 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. PetrovCurrent Protocols in Bioinformatics (2018) e51. doi: 10.1002/cpbi.51
- Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research
- Hufsky et al.Briefings in Bioinformatics (2020). doi: 10.1093/bib/bbaa232
- 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. PetrovNucleic 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. FinnNucleic 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. BatemanNucleic 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. BatemanRNA (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. BatemanNucleic 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. EddyNucleic Acids Research (2003) 31(1):p439-441
Covariance models and stochastic context-free grammars¶
- Annotating functional RNAs in genomes using Infernal
- E.P. NawrockiMethods in Molecular Biology (2014) 1097:163-97
- Infernal 1.1: 100-fold Faster RNA Homology Searches
- E. P. Nawrocki, S. R. EddyBioinformatics (2013) 29:2933-2935
- Computational Identification of Functional RNA Homologs in Metagenomic Data
- E. P. Nawrocki, S. R. EddyRNA Biology (2013) 10:1170-1179, 2013
- Infernal 1.0: Inference of RNA Alignments
- E.P. Nawrocki, D.L. Kolbe, S.R. EddyBioinformatics (2009) Mar 23. [Epub ahead of print]
- Local RNA Structure Alignment With Incomplete Sequence
- D.L. Kolbe, S.R. EddyBioinformatics (2009) Mar 20. [Epub ahead of print]
- Query-dependent banding (QDB) for faster RNA similarity searches
- E.P. Nawrocki, S.R. EddyPLoS 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. EddyBMC Bioinformatics (2002) 2(3):18
- Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
- R. Durbin, S.R. Eddy, A. Krogh, G. MitchisonCambridge 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. EddyNucleic Acids Research (1997) 25(5):955-964
- RNA sequence analysis using covariance models
- S.R. Eddy, R. DurbinNucleic Acids Research (1994) 22(11):2079-88