Rfam: an RNA family database

By Sam Griffiths-Jones, Alex Bateman, Mhairi Marshall, Ajay Khanna, Sean R. Eddy. 2003

1,636 citations recorded by the source corpus.

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

PMRD: plant microRNA database (2009, background): “... miRBase (http://microrna.sanger.ac.uk/), provides a set of precursor and mature miRNAs discovered in many plants (15); ASRP (http://asrp.cgrb .oregonstate.edu/) lists miRNAs and their target genes in Arabidopsis (16); CSRDB (http://sundarlab.ucdavis .edu/smrnas/) is a collection of miRNAs identi”
A benchmark of multiple sequence alignment programs upon structural RNAs (2005, methodology): “RNA structure analysis [1–5], RNA homology search [6, 7], ncRNA detection [8, 9] and RNA based phylogenetic inference [10, 11]).”
MicroRNA targets in Drosophila (2003, positive): “Given the surprisingly high level of sequence conservation of miRNAs across phyla [9,45], we assume that the set of miRNAs in D.”
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”
Fast and reliable prediction of noncoding RNAs (2005, positive): “Sequences for the test alignments were taken from the Rfam database [ 37 ] with the exception of the SRP and RNaseP test sets which were taken from other sources [48, 49] in order to use the same data as previous studies [22, 26].”
A uniform system for microRNA annotation. (2003, neutral): “An online clearinghouse for miRNA gene name assignments (http://www.sanger.ac.uk/Software/Rfam/mirna/) is provided by the Rfam database of RNA families ( Griffiths-Jones et al. 2003 ).”
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction (2004, neutral): “0 [52] [53] was graciously provided by Dave Mathews.”
4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing (2006, methodology): “Rfam [13] provides a method to compare a single nucleotide query sequence to handcurated alignments of non-coding RNA families with annotated consensus secondary structures.”
Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development (2004, neutral): “These were located by comparing the CNEs to the microRNA Registry [72] and the Rfam database (version 5.0) [ 73 ] using BLASTn [74].”
RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning (2019, background): “A 8.”
Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana (2004, background): “thaliana contains at least 22 miRNA families, most of which are conserved between monocots and dicot”
Computational prediction of miRNAs in Arabidopsis thaliana. (2005, methodology): “At the time the algorithm was run, the miRNA Registry held at Rfam in 2004 (http://www.sanger.ac.uk/Sofware/Rfam/mirna/; Griffiths-Jones et al. 2003; Griffiths-Jones 2004) contained 43 Arabidopsis miRNA precursors that could be grouped into 15 sequence-related precursor families (SRPF) as follows: M”
Rfam: Wikipedia, clans and the “decimal” release (2010, methodology): “Until then the mapping will remain rather coarse-grained and closely related to the existing types Rfam uses as annotation (6).”