JAR3D

JAR3D predicts three-dimensional geometries of RNA hairpin and internal loop sequences by matching them to motif groups in the RNA 3D Motif Atlas to inform analysis of non-coding RNA 3D motifs.

Key Features:

• Motif matching and scoring: Matches RNA sequences against motif groups in the RNA 3D Motif Atlas using exact sequence matches for structures observed in 3D and probabilistic scoring with edit distance for novel sequences.
• Probabilistic scoring: Assesses the likelihood of a sequence forming specific 3D interactions by evaluating patterns of non-Watson-Crick base pairs and base stacking.
• Comprehensive input handling: Accepts single-loop sequences, multiple loop sequences, and longer RNAs containing several loops for analysis.
• Output and alignment: Returns the ten best-matching motif groups per input sequence and can produce alignments between input sequences and motif groups.
• Dynamic updates: Updates its motif database in concert with each release of the RNA 3D Motif Atlas.

Scientific Applications:

• Non-coding RNA structure characterization: Predicts 3D geometries of hairpin and internal loops to aid interpretation of structured regions in non-coding RNAs.
• Motif annotation and transfer: Assigns input sequences to known 3D motif groups to infer structural interactions observed in experimentally determined structures.
• Novel motif exploration: Evaluates novel loop sequences with probabilistic scoring and edit distance to identify candidate 3D motifs for further study or modeling.

Methodology:

Matches sequences to motif groups from the RNA 3D Motif Atlas using exact sequence matching for known motifs and probabilistic scoring guided by edit distance metrics, with scoring that evaluates non-Watson-Crick base pairs and base stacking.