Non‐Coding RNA Analysis Using the Rfam Database

TLDR

Rfam is a freely available database of non‑coding RNA families, each represented by a multiple‑sequence alignment, consensus secondary structure, and covariance model, and its data support genome annotation and algorithm development. This article provides an overview of how to search and navigate the Rfam website and annotate sequences with RNA families. Rfam converts literature‑based RNA family descriptions into computational models through manual curation and a custom software pipeline, enabling annotation of RNAs in any DNA or RNA sequence. Rfam encapsulates valuable research outputs—often hidden in figures and supplementary files—into entries that are accessible via the Rfam website. © 2018 by John Wiley & Sons, Inc.

Abstract

Abstract Rfam is a database of non‐coding RNA families in which each family is represented by a multiple sequence alignment, a consensus secondary structure, and a covariance model. Using a combination of manual and literature‐based curation and a custom software pipeline, Rfam converts descriptions of RNA families found in the scientific literature into computational models that can be used to annotate RNAs belonging to those families in any DNA or RNA 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 Web site. The data produced by Rfam have a broad application, from genome annotation to providing training sets for algorithm development. This article gives an overview of how to search and navigate the Rfam Web site, and how to annotate sequences with RNA families. The Rfam database is freely available at http://rfam.org . © 2018 by John Wiley & Sons, Inc.