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PMID: 25392425 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Rfam 12.0: updates to the RNA families database.

Nucleic acids research ·Vol. 43 ·No. Database issue ·2015-01-00 ·Pages D130-7

Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD

Abstract

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.

MeSH Terms
Databases, Nucleic Acid Genomics Internet Molecular Sequence Annotation Nucleic Acid Conformation Nucleotide Motifs RNA, Long Noncoding/chemistry RNA, Untranslated/chemistry,classification Software
Chemicals
RNA, Long Noncoding RNA, Untranslated
Authors & Affiliations
11 authors, click to expand affiliations / ORCID
Nawrocki Eric P
HHMI Janelia Farm Research Campus, Ashburn, VA, USA.
Burge Sarah W
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Bateman Alex
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Daub Jennifer
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Eberhardt Ruth Y
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Eddy Sean R
HHMI Janelia Farm Research Campus, Ashburn, VA, USA.
Floden Evan W
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Gardner Paul P ORCID
Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
Jones Thomas A
HHMI Janelia Farm Research Campus, Ashburn, VA, USA.
Tate John
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Finn Robert D
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.
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gku1063
Email
rdf@ebi.ac.uk
Published
2015-01-00
Epub
2014-00-11
Pages
D130-7
Language
English
Region
England
NLM ID
0411011
PMCID
PMC4383904
Subset
IM
Grants
Wellcome Trust · WT098051 · United Kingdom
Howard Hughes Medical Institute · United States
External Links
PubMed source DOI: 10.1093/nar/gku1063 PMC Full Text View journal details
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