Rfam 12.0: updates to the RNA families database.
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.
HHMI Janelia Farm Research Campus, Ashburn, VA, USA.
Eric P
EP
Nawrocki
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Sarah W
SW
Burge
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Alex
A
Bateman
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Jennifer
J
Daub
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Ruth Y
RY
Eberhardt
HHMI Janelia Farm Research Campus, Ashburn, VA, USA.
Sean R
SR
Eddy
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Evan W
EW
Floden
Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
Paul P
http://orcid.org/0000-0002-7808-1213
PP
Gardner
HHMI Janelia Farm Research Campus, Ashburn, VA, USA.
Thomas A
TA
Jones
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
John
J
Tate
HHMI Janelia Farm Research Campus, Ashburn, VA, USA European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK rdf@ebi.ac.uk.
Robert D
RD
Finn
D030561:Databases, Nucleic Acid; D023281:Genomics; D020407:Internet; D058977:Molecular Sequence Annotation; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D062085:RNA, Long Noncoding / Q000737:chemistry; D022661:RNA, Untranslated / Q000737:chemistry* / Q000145:classification; D012984:Software
D062085:RNA, Long Noncoding; D022661:RNA, Untranslated