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Nucleic Acids Res. 2018 Jan 4;46(D1):D335-D342. doi: 10.1093/nar/gkx1038.

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

Author information

1
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
2
Systems Biology Graduate Program, Harvard University, Cambridge, MA 02138, USA.
3
National Center for Biotechnology Information; National Institutes of Health; Department of Health and Human Services; Bethesda, MD 20894, USA.
4
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
5
Howard Hughes Medical Institute, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.

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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