@article {46185,
	title = {Rfam 12.0: updates to the RNA families database.},
	journal = {Nucleic Acids Research},
	volume = {43},
	year = {2015},
	month = {2015 Jan 28},
	pages = {D130-7},
	abstract = {<p>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.</p>
},
	issn = {1362-4962},
	doi = {10.1093/nar/gku1063},
	author = {Nawrocki, Eric P and Burge, Sarah W and Bateman, Alex and Daub, Jennifer and Eberhardt, Ruth Y and Eddy, Sean R and Floden, Evan W and Gardner, Paul P and Jones, Thomas A and Tate, John and Finn, Robert D}
}
@article {6298,
	title = {Rfam 11.0: 10 years of RNA families.},
	journal = {Nucleic Acids Research},
	volume = {41},
	year = {2013},
	month = {2013 Jan},
	pages = {D226-32},
	abstract = {<p>The Rfam database (available via the website at http://rfam.sanger.ac.uk and through our mirror at http://rfam.janelia.org) is a collection of non-coding RNA families, primarily RNAs with a conserved RNA secondary structure, including both RNA genes and mRNA cis-regulatory elements. Each family is represented by a multiple sequence alignment, predicted secondary structure and covariance model. Here we discuss updates to the database in the latest release, Rfam 11.0, including the introduction of genome-based alignments for large families, the introduction of the Rfam Biomart as well as other user interface improvements. Rfam is available under the Creative Commons Zero license.</p>
},
	keywords = {Base Sequence, Databases, Genomics, Internet, Molecular Sequence Annotation, Nucleic Acid, Nucleic Acid Conformation, RNA, Sequence Alignment, Untranslated, User-Computer Interface},
	issn = {1362-4962},
	doi = {10.1093/nar/gks1005},
	author = {Burge, Sarah W and Daub, Jennifer and Eberhardt, Ruth and Tate, John and Barquist, Lars and Nawrocki, Eric P and Eddy, Sean R. and Gardner, Paul P and Bateman, Alex}
}
