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 updat...
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| Veröffentlicht in: | Nucleic acids research 2015-01, Vol.43 (Database issue), p.D130-D137 |
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| container_issue | Database issue |
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| container_title | Nucleic acids research |
| container_volume | 43 |
| creator | Nawrocki, Eric P Burge, Sarah W Bateman, Alex Daub, Jennifer Eberhardt, Ruth Y Eddy, Sean R Floden, Evan W Gardner, Paul P Jones, Thomas A Tate, John Finn, Robert D |
| description | 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. |
| doi_str_mv | 10.1093/nar/gku1063 |
| format | Article |
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| subjects | Database Issue Databases, Nucleic Acid Genomics Internet Molecular Sequence Annotation Nucleic Acid Conformation Nucleotide Motifs RNA, Long Noncoding - chemistry RNA, Untranslated - chemistry RNA, Untranslated - classification Software |
| title | Rfam 12.0: updates to the RNA families database |
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