Rfam search with JAR3D Search for RNA 3D Motifs in Rfam

Internal Loop Examples

• Kink turn internal loop
• Sarcin-ricin internal loop
• Double sheared pair internal loop
• Triple sheared pair internal loop
• C-loop internal loop
• UAA/GAN internal loop
• Receptor of 11nt loop-receptor internal loop
• Tandem non-canonical cWW pair internal loop
• Bacterial 5S loop E internal loop

Hairpin Loop Examples

• GNRA hairpin loop
• UNCG hairpin loop
• T-loop hairpin loop
• tRNA anticodon hairpin loop
• tRNA D-loop hairpin loop

About JAR3D

JAR3D scores RNA hairpin and internal loop sequences against motif groups from the RNA 3D Motif Atlas, by exact sequence match for sequences already observed in 3D and by probabilistic scoring and edit distance for novel sequences.

RNA hairpin and internal loops are often represented on secondary structure diagrams as if they are unstructured, but in fact most are structured by non-Watson-Crick basepairs, base stacking, and base-backbone interactions. Analysis of 3D structures shows that different RNA sequences can form the same RNA 3D motif, as is apparent in many motif groups in the RNA 3D Motif Atlas.

JAR3D scores sequences to motif groups based on the ability of the sequences to form the same pattern of interactions observed in 3D structures of the motif. As RNA 3D Motif Atlas incorporates new RNA 3D structures, the performance of JAR3D will improve over time.

Inferring the 3D structures of hairpin and internal loops is a step on the way toward correctly predicting full RNA 3D structures starting from sequence.

More About JAR3D

At the JAR3D Homepage you can search for motif group matches in single sequencs, multiple sequence alignments, or Rfam seed alignments.

Learn more about JAR3D in the tutorial.

Rfam Search Input

The JAR3D Rfam search accepts single or multiple RNA 3D Motif Atlas internal loop and hairpin loop motif group IDs from a supported RNA 3D Motif Atlas release. Currently the supported RNA 3D Motif Atlas releases are 3.48 and 3.9. The RNA 3D Motif Atlas may have multiple motif groups for related loop structures, due to differences in geometry. For example, in Motif Atlas release 3.48 there are four groups for kink turns. To facilitate searching for all kink turns in Rfam families, multiple RNA 3D Motif Atlas motif group IDs may be entered into the search at once.

The Examples section above will fill in RNA 3D Motif Atlas motif group IDs for a number of common internal and hairpin loop structures. You can also search the most recent supported release of the RNA 3D Motif Atlas for internal loops or hairpin loops.

Rfam Search Output

The output shows the loops from Rfam families that have an acceptance rate of 80% or higher for the JAR3D group for the searched RNA 3D Motif Atlas motif group ID. Links are provided to full JAR3D search results, as well as to the motif group the match was made to. Also shown are JAR3D match statistics cutoff rate, mean cutoff score, and median full and interior edit distance. Finally, two counts for PDB chains matching the Rfam family are shown, one for the number of matches when the RNA 3D Motif Atlas release used for the search, and one for all chains currently in the PDB.

Rfam Search Method

1. We retrieve all seed alignments from Rfam, with the exception of ribosomal families, as the alignments are too large.

2. For select JAR3D releases, loops are extracted from the Rfam seed alignments and scored against JAR3D models, using the Rfam consensus secondary structure.

3. When an RFAM-JAR3D search is initiated, we retrieve all loops from Rfam families for which at least 80% of the loops in the seed alignment are accepted by the JAR3D model.

For more information please see:

Identifying novel sequence variants of RNA 3D motifs. Craig L. Zirbel, James Roll, Blake A. Sweeney, Anton I. Petrov, Meg Pirrung, and Neocles Leontis. Nucl. Acids Res. (2015) doi: 10.1093/nar/gkv651 Pubmed

Standalone version of JAR3D is also available.