Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

The Rfam database is a collection of RNA families in which each family is represented by a multiple sequence alignment, a consensus secondary structure, and a covariance model. In this paper we introduce Rfam release 13.0, which switches to a new genome-centric approach that annotates a non-redundan...

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Autores principales: Kalvari, Ioanna, Argasinska, Joanna, Quinones-Olvera, Natalia, Nawrocki, Eric P, Rivas, Elena, Eddy, Sean R, Bateman, Alex, Finn, Robert D, Petrov, Anton I
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Database Issue
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753348/
https://www.ncbi.nlm.nih.gov/pubmed/29112718
http://dx.doi.org/10.1093/nar/gkx1038
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author Kalvari, Ioanna
Argasinska, Joanna
Quinones-Olvera, Natalia
Nawrocki, Eric P
Rivas, Elena
Eddy, Sean R
Bateman, Alex
Finn, Robert D
Petrov, Anton I
author_facet Kalvari, Ioanna
Argasinska, Joanna
Quinones-Olvera, Natalia
Nawrocki, Eric P
Rivas, Elena
Eddy, Sean R
Bateman, Alex
Finn, Robert D
Petrov, Anton I
author_sort Kalvari, Ioanna
collection PubMed
description The Rfam database is a collection of RNA families in which each family is represented by a multiple sequence alignment, a consensus secondary structure, and a covariance model. In this paper we introduce Rfam release 13.0, which switches to a new genome-centric approach that annotates a non-redundant set of reference genomes with RNA families. We describe new web interface features including faceted text search and R-scape secondary structure visualizations. We discuss a new literature curation workflow and a pipeline for building families based on RNAcentral. There are 236 new families in release 13.0, bringing the total number of families to 2687. The Rfam website is http://rfam.org.
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spelling pubmed-57533482018-01-05 Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families Kalvari, Ioanna Argasinska, Joanna Quinones-Olvera, Natalia Nawrocki, Eric P Rivas, Elena Eddy, Sean R Bateman, Alex Finn, Robert D Petrov, Anton I Nucleic Acids Res Database Issue The Rfam database is a collection of RNA families in which each family is represented by a multiple sequence alignment, a consensus secondary structure, and a covariance model. In this paper we introduce Rfam release 13.0, which switches to a new genome-centric approach that annotates a non-redundant set of reference genomes with RNA families. We describe new web interface features including faceted text search and R-scape secondary structure visualizations. We discuss a new literature curation workflow and a pipeline for building families based on RNAcentral. There are 236 new families in release 13.0, bringing the total number of families to 2687. The Rfam website is http://rfam.org. Oxford University Press 2018-01-04 2017-11-03 /pmc/articles/PMC5753348/ /pubmed/29112718 http://dx.doi.org/10.1093/nar/gkx1038 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
Kalvari, Ioanna
Argasinska, Joanna
Quinones-Olvera, Natalia
Nawrocki, Eric P
Rivas, Elena
Eddy, Sean R
Bateman, Alex
Finn, Robert D
Petrov, Anton I
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
title Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
title_full Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
title_fullStr Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
title_full_unstemmed Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
title_short Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
title_sort rfam 13.0: shifting to a genome-centric resource for non-coding rna families
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753348/
https://www.ncbi.nlm.nih.gov/pubmed/29112718
http://dx.doi.org/10.1093/nar/gkx1038
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