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JAR3D specifications


Unique identifier OMICS_11979
Name JAR3D
Alternative name Java-based Alignment of RNA using 3D structure
Interface Web user interface
Restrictions to use None
Input data JAR3D accepts single or multiple sequences with one or many loops.
Output data 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.
Computer skills Basic
Stability Stable
Maintained Yes



  • person_outline Craig L. Zirbel


Unique identifier OMICS_11979
Name JAR3D
Alternative name Java-based Alignment of RNA using 3D structure
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, MATLAB, Python
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Craig L. Zirbel

Publications for Java-based Alignment of RNA using 3D structure

JAR3D citations


Allelic RNA Motifs in Regulating Systemic Trafficking of Potato Spindle Tuber Viroid

PMCID: 5923454
PMID: 29601476
DOI: 10.3390/v10040160

[…] 19 structural analyses because using this simple loop as a bait for sequence homology-based search retrieved too many possible structures with similar likelihood scores when using the latest program JAR3D []. To circumvent this difficulty, we relied on the sequences of the six functional variants and assumed that these functional variants are isosteric. This assumption was based on the latest kno […]


Computational Methods for Modeling Aptamers and Designing Riboswitches

Int J Mol Sci
PMCID: 5713409
PMID: 29149090
DOI: 10.3390/ijms18112442
call_split See protocol

[…] d to reflect the native fold of the RNA. Taking the aptamer from Fusobacterium nucleatum double glycine riboswitch as an example, the Rosetta 3D modeling can give a similar prediction as RMdetect and JAR3D [,,,].Also, starting from 2D structures, a hierarchical computational approach (RAGTOP) was modified to predict 10 representative riboswitch aptamers with diverse structural features [], by comb […]


Using sequence signatures and kink turn motifs in knowledge based statistical potentials for RNA structure prediction

Nucleic Acids Res
PMCID: 5435971
PMID: 28158755
DOI: 10.1093/nar/gkx045

[…] found that predictions improve using various motif search tools, such as a sequence-based motif prediction tool RMDetect () that can search for G-bulge loop, kink-turn, C-loop and tandem-GA loop; or JAR3D () that searches RNA motifs. However, these tools are not currently integrated with structure prediction tools for RNA. Nonetheless, as the RNA motif world becomes more annotated, sequence signa […]


Trends and challenges in computational RNA biology

Genome Biol
PMCID: 5141647
PMID: 27927225
DOI: 10.1186/s13059-016-1117-7

[…] amics simulations. Other talks described approaches that instead use auxiliary data to bypass the difficult step of molecular simulations. Craig Zirbel (Bowling Green State University, USA) described JAR3D, a set of probabilistic models parametrized on the RNA 3D Motif Atlas, that infer new 3D motifs from sequences. Debora Marks (Harvard Medical School, USA) described how evolutionary couplings ca […]


RNA 3D Modules in Genome Wide Predictions of RNA 2D Structure

PLoS One
PMCID: 4624896
PMID: 26509713
DOI: 10.1371/journal.pone.0139900

[…] results of the enrichment analysis show that a fraction of MmrmIL, MjarIL, and MjarHL are significantly enriched. The FETfixpscore identifies 8 out of 63 (12.7%) distinct mRmIL, 13 out of 276 (4.7%) JAR3D IL, and 28 out of 253 (11.1%) JAR3D HL models that predict 3D modules that are significantly enriched (adjusted p-value ≤ 0.05, see Tables C–H in ). Requiring an odds ratio of at least 1.25 resu […]


High throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase

Nucleic Acids Res
PMCID: 3561961
PMID: 23241386
DOI: 10.1093/nar/gks1190

[…] ak in a highly variable region that does not contact RT in the corresponding F1Pk-RT co-crystal structure.For the newly identified (6/5)AL motif, a structural bioinformatics search using the software JAR3D () identified multiple asymmetric loops of the same size and related sequence composition as the (6/5)AL internal loop within functionally unrelated reference RNAs. Within those reference struct […]


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JAR3D institution(s)
Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH, USA; Department of Biology, Bowling Green State University, Bowling Green, OH, USA; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Chemistry, Bowling Green State University, Bowling Green, OH, USA
JAR3D funding source(s)
National Institutes of Health (NIH) [GM085328]

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