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

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5753348.pdf (2.95 MB)

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2018

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10.1093/nar/gkx1038

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Oxford University Press
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Kalvari, Ioanna, Joanna Argasinska, Natalia Quinones-Olvera, Eric P Nawrocki, Elena Rivas, Sean R Eddy, Alex Bateman, Robert D Finn, and Anton I Petrov. 2018. “Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.” Nucleic Acids Research 46 (Database issue): D335-D342. doi:10.1093/nar/gkx1038. http://dx.doi.org/10.1093/nar/gkx1038.

Abstract

Abstract 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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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753348/pdf/

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http://nrs.harvard.edu/urn-3:HUL.InstRepos:34869070

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