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Rfam 12.0: updates to the RNA families database.

TitleRfam 12.0: updates to the RNA families database.
Publication TypeJournal Article
Year of Publication2015
AuthorsNawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, Finn RD
JournalNucleic Acids Res
Volume43
IssueDatabase issue
PaginationD130-7
Date Published2015 Jan
ISSN1362-4962
KeywordsDatabases, Nucleic Acid, Genomics, Internet, Molecular Sequence Annotation, Nucleic Acid Conformation, Nucleotide Motifs, RNA, Long Noncoding, RNA, Untranslated, Software
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.

DOI10.1093/nar/gku1063
Alternate JournalNucleic Acids Res.
PubMed ID25392425
PubMed Central IDPMC4383904
Grant ListWT098051 / / Wellcome Trust / United Kingdom
/ / Howard Hughes Medical Institute / United States