Rfam 12.0: updates to the RNA families database.
Bottom Line: 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.
Affiliation: HHMI Janelia Farm Research Campus, Ashburn, VA, USA.Show MeSH
Mentions: On the Rfam website, information for each motif can be accessed via individual motif pages. These contain tabs for a Wikipedia article, seed alignments, structures, family matches, references and a curation tab. The page for the Terminator1 motif (RM00022) is shown in Figure 2 as an example. In addition to this, a tab has been added to each family page, displaying the motifs, if any, that match the family. Motif annotations for a family can be visualized by overlaying motif matches on the secondary structure image for the family. For each position of the secondary structure image, the fraction of seed sequences that match a selected motif is calculated and is represented on the structure image using a rainbow scale. Figure 3 gives an example, showing the secondary structure for the RsmY family (RF00195) overlaid with CsrA binding motif (RM00005) annotation. The interaction of RsmY with the RNA binding protein CsrA via this motif is part of a post-transcriptional regulatory network in gammaproteobacteria (23,24).
Affiliation: HHMI Janelia Farm Research Campus, Ashburn, VA, USA.