Rfam: Wikipedia, clans and the “decimal” release

By Paul P. Gardner, Jennifer Daub, John G. Tate, Benjamin L. Moore, Isabelle H. Osuch, Sam Griffiths-Jones, Robert D. Finn, Eric P. Nawrocki, Diana L. Kolbe, Sean R. Eddy and 1 more. Nucleic Acids Res., 2010

414 citations recorded by the source corpus.

The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models. In this contribution, we discuss the pros and cons of using the online encyclopedia, Wikipedia, as a source of community-derived annotation. We discuss the addition of groupings of related RNA families into clans and new developments to the website. Rfam is available on the Web at http://rfam.sanger.ac.uk.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d49d38b1083f4d2485a7982108221eac5541e2c1

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Citations in the corpus

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases (2020, methodology): “The Rfam results are post-processed to select the top scoring families from the same Rfam clan (16).”
nhmmer: DNA homology search with profile HMMs (2013, positive): “The benchmark consists of 106 families from Rfam that could be divided into two groups such that no sequence in one group is460% identical to any sequence in the other group [Rfam 10.0, Gardner et al. (2011)].”
RNA secondary structure prediction using deep learning with thermodynamic integration (2020, background): “0 (32), which contain 22 families with 3D structure annotations.”
LNCipedia: a database for annotated human lncRNA transcript sequences and structures (2012, background): “Rfam provides structures and annotation of well-known RNA families along with predictions of new members of these families (14).”
Non-coding RNA analysis using the Rfam database (2018, neutral): “Rfam organizes related families into clans (Gardner et al., 2011).”