JAR3D Scoring RNA loop sequences against known 3D motifs Tutorial

Examples

• Single sequence, one loop
• Multiple sequences, one loop
• Multiple sequences, one loop (fasta)
• Single sequence, many loops, with secondary structure
• Single sequence, many loops, with secondary structure (fasta)
• Multiple sequences, many loops, with secondary structure
• Multiple sequences, many loops, with secondary structure (fasta)
• Rfam family

About

JAR3D scores RNA hairpin and internal loop and 3-way and 4-way junction 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 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 loops is a step on the way toward correctly predicting full RNA 3D structures starting from sequence.

Rfam

You can use JAR3D to search for known 3D motifs across all Rfam seed alignments at Rfam search with JAR3D page.

Tutorial

Learn more about JAR3D in the tutorial.

Input

JAR3D accepts single or multiple sequences with one or many loops (see Examples above).

One loop: To specify the break between strands in internal loops, use an asterisk *. Sequence(s) without an asterisk are interpreted as hairpins. Internal and hairpin loops should include closing Watson-Crick basepairs, with nucleotides running in 5' to 3' order within each strand. Individual loops do not need the nucleotides to be aligned.

Many loops: JAR3D will extract internal and hairpin loops from longer sequences if a dot-bracket secondary structure is provided as the first line of the input. Multiple sequences need to be aligned to one another.

Rfam: You can input an Rfam identifier to see motif matches for all loops in the Rfam secondary structure.

Several online services can predict RNA secondary structure and provide output that can be used as input to JAR3D, for example: RNAfold, UNAFold, or LocaRNA.

Output

The output shows the best-scoring motif groups from the RNA 3D Motif Atlas including representative instance from each motif group. It also possible to align input sequences to known 3D instances of a motif.

Method

1. We extract hairpin and internal loops and junctions from a representative set of RNA 3D structures at 3.5 Angstrom resolution or better from PDB and cluster them into geometrically similar motif groups.

2. For each motif group, we build a probabilistic model for sequence variability based on a hybrid Stochastic Context-Free Grammar/Markov Random Field (SCFG/MRF) method.

3. To parameterize each model, we use all instances of the motif found in the motif group and knowledge of RNA nucleotide interactions, especially isosteric basepairs and their substitution patterns.

4. For each motif group, we form an acceptance region that is consistent with the geometry and basepairing of that group. If the score is in the cutoff region, we infer that the new sequence can form the same 3D structure.

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

JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs. James Roll, Craig L. Zirbel, Blake A. Sweeney, Anton I. Petrov, and Neocles Leontis. Nucl. Acids Res. (2016) doi: 10.1093/nar/gkw453

A standalone version of JAR3D is also available on GitHub.