Rfam: annotating non-coding RNAs in complete genomes

By Sam Griffiths-Jones, Simon Moxon, Mhairi Marshall, Ajay Khanna, Sean R. Eddy, Alex Bateman. Nucleic Acids Res., 2004

1,741 citations recorded by the source corpus.

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/.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/dc5a592cbbf92008ee5a565de9164c94de2fdde3

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Citations in the corpus

Rfam: updates to the RNA families database (2008, methodology): “The Rfam database was developed as a generic approach to the annotation of structured RNA families on genomic sequences (2,3), but it has been widely used as a source of reliable alignments and structures for the purposes of training and benchmarking RNA sequence and secondary structure analysis sof”
GtRNAdb: a database of transfer RNA genes detected in genomic sequence (2008, methodology): “Users will be able to download gene information in various file formats, including the BED format developed for the UCSC Genome Browser (5), and the Stockholm format used in Pfam (12) and Rfam (13) for multiple sequence and secondary structure alignments.”
RNAmmer: consistent and rapid annotation of ribosomal RNA genes (2007, result): “RFAM is a database of RNA families which incorporates secondary structure in its analyses.”
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation (2007, background): “Several of these riboswitches have been experimentally described and their sequences are obtained from Rfam, a database of RNA families (9).”
Query-Dependent Banding (QDB) for Faster RNA Similarity Searches (2007, methodology): “The Rfam database of RNA families [17] is based on CM software (Infernal [inference of RNA alignment]; http:// infernal.”
IMG: the integrated microbial genomes database and comparative analysis system (2011, background): “The ‘Abundance Profile Overview’ allows users to compare the relative abundance of protein families (COGs, Pfams, TIGRfams) and functional families (enzymes) across selected genomes, whereby the results are displayed either as a heat map or a matrix, with the cells in the heat map and matrix linked ”
A Bioinformatician's Guide to Metagenomics (2008, background): “Other types of noncoding RNA (ncRNA) genes can be detected by comparison to covariance models (55) and sequence-structure motifs (84).”
The Emerging Field of RNA Nanotechnology (2010, positive): “A rich resource of well-developed databases can be used to extract known RNA structural units for the construction of new RNA nanoparticles with desired propertie”