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Rfam: Annotating Non-coding RNAs In Complete Genomes

S. Griffiths-Jones, S. Moxon, M. Marshall, Ajay Khanna, S. Eddy, A. Bateman
Published 2004 · Biology, Medicine, Computer Science

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Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the identification and classification of new members of known sequence families, and distributes annotation of ncRNAs in over 200 complete genome sequences. The data provide the first glimpses of conservation of multiple ncRNA families across a wide taxonomic range. A small number of large families are essential in all three kingdoms of life, with large numbers of smaller families specific to certain taxa. Recent improvements in the database are discussed, together with challenges for the future. Rfam is available on the Web at http://www.sanger.ac.uk/Software/Rfam/ and http://rfam.wustl.edu/.
This paper references
10.1146/ANNUREV.BI.55.070186.003215
Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information.
A. Weiner (1986)
10.1093/NAR/25.17.3389
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
S. Altschul (1997)
10.1038/35057062
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium (2001)
10.1038/35057062
Initial sequencing and analysis of the human genome.
E. Lander (2001)
10.1038/nature01262
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002)
10.1016/S0300-9084(02)01402-5
The expanding snoRNA world.
J. P. Bachellerie (2002)
10.1186/1471-2105-3-18
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure
S. Eddy (2002)
10.1038/NATURE01262
Initial sequencing and comparative analysis of the mouse genome.
R. Waterston (2002)
10.1016/S0092-8674(02)00905-4
An RNA Thermosensor Controls Expression of Virulence Genes in Listeria monocytogenes
J. Johansson (2002)
A memoryefficient dynamic programming algorithm for optimal alignment of a sequence to anRNAsecondary structure
S. R. Eddy (2002)
2002)AnRNA thermosensor controls expressionof virulence genes in Listeria monocytogenes
J. Johansson (2002)
10.1371/journal.pbio.0000045
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
L. Stein (2003)
10.1093/NAR/GKG297
A survey of small RNA-encoding genes in Escherichia coli.
R. Hershberg (2003)
10.1093/nar/gkg006
Rfam: an RNA family database
S. Griffiths-Jones (2003)
Rfam : anRNA family database
S. Griffiths-Jones (2003)
Rfam : anRNA family database
M. Mandal (2003)
10.1016/S0092-8674(04)00045-5
MicroRNAs Genomics, Biogenesis, Mechanism, and Function
D. Bartel (2004)
10.1016/J.TIG.2003.11.008
Riboswitches: the oldest mechanism for the regulation of gene expression?
A. Vitreschak (2004)
10.1016/J.MIB.2004.02.015
Controlling mRNA stability and translation with small, noncoding RNAs.
G. Storz (2004)
10.1093/bioinformatics/bth925
Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy
Z. Weinberg (2004)
10.1038/nature03154
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
L. Hillier (2004)
10.1073/PNAS.0402424101
Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors.
K. Bell (2004)
10.1038/nrm1403
Gene regulation by riboswitches
Maumita Mandal (2004)
D124 Nucleic Acids Research
(2005)



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