Rfam 12.0: updates to the RNA families database

Abstract

The Rfam database (available at http://rfam.xfam.org) is a collection of non-coding RNA families represented by manually curated sequence alignments, consensus secondary structures and annotation gathered from corresponding Wikipedia, taxonomy and ontology resources. In this article, we detail updates and improvements to the Rfam data and website for the Rfam 12.0 release. We describe the upgrade of our search pipeline to use Infernal 1.1 and demonstrate its improved homology detection ability by comparison with the previous version. The new pipeline is easier for users to apply to their own data sets, and we illustrate its ability to annotate RNAs in genomic and metagenomic data sets of various sizes. Rfam has been expanded to include 260 new families, including the well-studied large subunit ribosomal RNA family, and for the first time includes information on short sequence- and structure-based RNA motifs present within families.

Figure 1.

Number of Rfam family matches for each of the 34 RMfam motifs.

Figure 2.

Overview of the motif page for RM00022, the Terminator1 motif, on the Rfam 12.0 website. As in family and clan pages, tabs on the left-hand side allow the user to access different information for each motif.

Figure 3.

Screenshot of the secondary structure representation for the RsmY RNA family (RF00195) with the annotation for the CsrA binding motif (RM00005) overlaid. Positions in red indicate that all the seed sequences at that position are found to contain the motif while other colours represent fewer sequences having matches at that position. The CsrA protein is a homo-dimeric, RNA binding protein. Each CsrA binds a specific RNA motif that is characterized by a short hairpin that hosts a GGA subsequence, these motifs generally occur in pairs. The CsrA-binding sRNAs, like RsmY, generally sequester excess copies of CsrA which would otherwise bind mRNAs and inhibit translation (23). Therefore, the expression of these sRNAs is a rapid way of altering expression levels for a potentially large network of proteins (24).