Rfam 12.0: updates to the RNA families database

By Eric P. Nawrocki, Sarah W. Burge, Alex Bateman, Jennifer Daub, R. Y. Eberhardt, Sean R. Eddy, E. Floden, Paul P. Gardner, Thomas A. Jones, John G. Tate and 1 more. 2014

1,037 citations recorded by the source corpus.

The Rfam database (available at http://rfam.xfam.org) is a collection of non-coding RNA families represented by manually curated sequence alignments, consensus secondary structures and annotation gathered from corresponding Wikipedia, taxonomy and ontology resources. In this article, we detail updates and improvements to the Rfam data and website for the Rfam 12.0 release. We describe the upgrade of our search pipeline to use Infernal 1.1 and demonstrate its improved homology detection ability by comparison with the previous version. The new pipeline is easier for users to apply to their own data sets, and we illustrate its ability to annotate RNAs in genomic and metagenomic data sets of various sizes. Rfam has been expanded to include 260 new families, including the well-studied large subunit ribosomal RNA family, and for the first time includes information on short sequence- and structure-based RNA motifs present within families.

Subfields: Molecular Biology

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Citations in the corpus

NCBI prokaryotic genome annotation pipeline (2016, methodology): “Genes of ribosomal RNAs were predicted either by the BLASTn sequence similarity search using the entries from the RNA sequence database as queries or by running specialized tools, such as Infernal (5,6) and Rfam (7).”
Ensembl 2021 (2020, methodology): “To enrich our gene structure annotation, we have added structural RNAs from Rfam (40), full cross-references to annotated entries at Uniprot (41) and RefSeq, functional annotation from the Gene Ontology Consortium (42), and annotation of protein domains from InterProScan.”
Rfam 14: expanded coverage of metagenomic, viral and microRNA families (2020, methodology): “The new search also performs the clan competition procedure (49) which selects the longest and highest scoring hit if several Rfam families from the same clan match the query sequence.”
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation (2015, background): “Our goals for the coming year include greater integration of Rfam (65) in our annotation pipeline, expanded collaboration, improved protein names, and reporting support evidence on the protein sequence record.”
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation (2016, methodology): “Otherwise we revert to using Rfam (38), mirbase (39), UniProt or EntrezGene (40) names and, if there is no other option, a clone name.”
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families (2017, methodology): “Search results from models in the same clan often overlap so in Rfam we analyse the overlaps and report only the lowest-scoring hits using a procedure called ‘clan competing’ (8).”
3D RNA and Functional Interactions from Evolutionary Couplings. (2015, positive): “Another area for future research is to build on the outstanding work of the RFAM database (Nawrocki et al., 2015) by extending sequence coverage and including more transcripts that potentially have 3D structure.”
Non-coding RNA analysis using the Rfam database (2018, background): “Infernal’s scoring sys-tem is designed to recognize homology by sequence similarity, and some RNA pseudo-genes are similar enough to the functional RNA genes they derive from to score above Rfam GA thresholds and/or with statistically signiﬁcant E-values.”
The EBI search engine: EBI search as a service—making biological data accessible for all (2017, background): “Since last reported, new data resources include the Enzyme Portal (3), providing protein- and enzyme-centric views; Rfam (4) RNA families; Ensembl Genome Variants (5); Elixir Tools Registry (6); Omics Discovery Index (OmicsDI) (https://doi.org/10.”
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation (2020, methodology): “In addition, 49 Rfam models for small, non-coding RNA features that are known to be found in prokaryotes, such as riboswitches and attenuators (see list in Supplementary Table S1) are searched in all genomes using Infernal cmsearch (9).”