title: JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.
abstract: Many non-coding RNAs have been identified and may function by forming 2D and 3D structures. RNA hairpin and internal loops are often represented as unstructured on secondary structure diagrams, but RNA 3D structures show that most such loops are structured by non-Watson-Crick basepairs and base stacking. Moreover, different RNA sequences can form the same RNA 3D motif. JAR3D finds possible 3D geometries for hairpin and internal loops by matching loop sequences to motif groups from the RNA 3D Motif Atlas, by exact sequence match when possible, and by probabilistic scoring and edit distance for novel sequences. The scoring gauges the ability of the sequences to form the same pattern of interactions observed in 3D structures of the motif. The JAR3D webserver at http://rna.bgsu.edu/jar3d/ takes one or many sequences of a single loop as input, or else one or many sequences of longer RNAs with multiple loops. Each sequence is scored against all current motif groups. The output shows the ten best-matching motif groups. Users can align input sequences to each of the motif groups found by JAR3D. JAR3D will be updated with every release of the RNA 3D Motif Atlas, and so its performance is expected to improve over time.
authors.affiliation: Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA.
authors.forename: James
authors.initials: J
authors.lastname: Roll
authors.affiliation: Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA zirbel@bgsu.edu.
authors.forename: Craig L
authors.initials: CL
authors.lastname: Zirbel
authors.affiliation: Department of Biology, Bowling Green State University, Bowling Green, OH 43403, USA.
authors.forename: Blake
authors.initials: B
authors.lastname: Sweeney
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Anton I
authors.identifier: 0000-0001-7279-2682
authors.initials: AI
authors.lastname: Petrov
authors.affiliation: Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA.
authors.forename: Neocles
authors.initials: N
authors.lastname: Leontis
mesh_terms: D020029:Base Pairing; D003196:Computer Graphics; D020407:Internet; D015233:Models, Statistical; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D059370:RNA Folding; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D014584:User-Computer Interface
chemical_list: D012313:RNA