Rfam: updates to the RNA families database

By Paul P. Gardner, Jennifer Daub, John G. Tate, Eric P. Nawrocki, Diana L. Kolbe, Stinus Lindgreen, A. Wilkinson, Robert D. Finn, Sam Griffiths-Jones, Sean R. Eddy and 1 more. Nucleic Acids Res., 2008

934 citations recorded by the source corpus.

Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs). The primary aim of Rfam is to annotate new members of known RNA families on nucleotide sequences, particularly complete genomes, using sensitive BLAST filters in combination with CMs. A minority of families with a very broad taxonomic range (e.g. tRNA and rRNA) provide the majority of the sequence annotations, whilst the majority of Rfam families (e.g. snoRNAs and miRNAs) have a limited taxonomic range and provide a limited number of annotations. Recent improvements to the website, methodologies and data used by Rfam are discussed. Rfam is freely available on the Web at http://rfam.sanger.ac.uk/and http://rfam.janelia.org/.

Subfields: Molecular Biology

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Citations in the corpus

Rfam: Wikipedia, clans and the “decimal” release (2010, background): “Of particular note are the direct submissions of Stockholm formatted alignments and corresponding Wikipedia articles from the RNA community via the RNA families track at RNA Biology (8).”
MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations1[W][OPEN] (2013, background): “, 2009), a stochastic context-free grammar (SCFG) based general ncRNA search tool to identify ncRNA homologs to annotated ncRNA families in Rfam (Gardner et al., 2009).”
miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments (2009, neutral): “0 (18) were downloaded from http://rfam.”
RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria (2013, methodology): “First, RNA regulatory sites were identified in the studied genomes using the probabilistic covariance models for 43 RNA families from the Rfam database [28] and the Infernal program [29].”
Metagenomic Analyses: Past and Future Trends (2010, positive): “Thirteen known sRNA families were identified in the metatranscriptomic data set by searching the RNA family database Rfam (35).”
Metagenomics - a guide from sampling to data analysis (2012, background): “There exists also a number of tools for the prediction of non-protein coding genes such as tRNAs [66,67], signal peptides [68] or CRISPRs [69,70], however they might require significant computational resources or long contiguous sequences.”
Prediction of microRNAs Associated with Human Diseases Based on Weighted k Most Similar Neighbors (2013, background): “The homologous miRNAs are gathered into the same miRNA family by RFam [32].”
A survey of best practices for RNA-seq data analysis (2016, methodology): “The Rfam database [118] contains most well-characterized RNA families, such as ribosomal or transfer RNAs, while mirBase [119] or Miranda [120] are specialized in miRNAs.”
A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti (2010, background): “meliloti, four suhB paralogs were identified [34].”
Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis (2012, background): “subtilis genome annotation, 57 5’ cis-acting structures are identified by a scan of the genome sequence against the RFAM database of RNA families (36).”
The Ensembl gene annotation system (2016, methodology): “In order to annotate small ncRNA genes, sequences from Rfam (83) are first aligned to the genome using BLASTN.”
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells (2011, methodology): “We extracted rRNA sequences from GenBank 44 and other non-coding RNA sequences from Rfam 46 .”
The functional role of long non-coding RNA in human carcinomas (2011, neutral): “uk/ [251]”
ViennaRNA Package 2.0 (2011, background): “Due to the wide-spread use of the STOCKHOLM format in RNA bioinformatics, e.g. in the Rfam - RNA family data-base [82]), support for *.stk files has been added.”
An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs (2013, methodology): “Rfam [4,5] is a database comprehensively collecting families of non-coding RNA (ncRNA) genes as well as cisregulatory RNA elements.”
Infernal 1.0: inference of RNA alignments (2009, methodology): “One use of INFERNAL is to annotate RNAs in genomes in conjunction with the RFAM database [16], which contains hundreds of RNA families.”
ModeRNA: a tool for comparative modeling of RNA 3D structure (2011, methodology): “Pairwise target–template alignments used for tRNA modeling were extracted from the Rfam database (4).”
miRBase: integrating microRNA annotation and deep-sequencing data (2010, methodology): “The Rfam database of RNA families (17) has successfully developed a community annotation project using Wikipedia (18).”