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 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 (2008) 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

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, 2013
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