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.
Highlights
Rfam is a database of RNA families in which each family is represented by a multiple sequence alignment, a consensus secondary structure, and a covariance model (CM)
Using a combination of manual, literature-based curation and a custom software pipeline, Rfam converts descriptions of RNA families found in research papers into computational models that can be used to annotate RNAs belonging to those families in any DNA sequence
Valuable research outputs that are often locked up in figures and supplementary information files are encapsulated in Rfam entries and made accessible through the Rfam website and other resources that integrate the Rfam data, such as Ensembl (1) and UCSC (2) genome browsers
Summary
Rfam is a database of RNA families in which each family is represented by a multiple sequence alignment, a consensus secondary structure, and a covariance model (CM). The process of building a new Rfam family starts with extracting RNA sequences and, where possible, sequence alignments and secondary structures, from the scientific literature and manually building a seed alignment. Rfam uses the Infernal software package (3) to build CMs and perform iterative sequenceand secondary structure-based searches against a sequence database to find other instances of the family.
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
