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Junction-Explorer specifications


Unique identifier OMICS_16329
Name Junction-Explorer
Interface Application programming interface
Restrictions to use None
Input data An RNA sequence and its secondary structure.
Input format bpseq, CT, vienna dot-bracket
Output data The web server displays a table for each identified junction. (If no junction is identified, the web server displays a message indicating so.)
Computer skills Advanced
Stability Stable
Maintained Yes



  • person_outline Tamar Schlick

Publication for Junction-Explorer

Junction-Explorer citations


Phylogenetic Reconstruction of the Calosphaeriales and Togniniales Using Five Genes and Predicted RNA Secondary Structures of ITS, and Flabellascus tenuirostris gen. et sp. nov.

PLoS One
PMCID: 4689446
PMID: 26699541
DOI: 10.1371/journal.pone.0144616

[…] the topology of three-way junction (family a, b or c) occurring in the determined its1 model and also predicted coaxial helical stacking arrangement in the junction. the freely available programs junction explorer [] and cartaj [] were used for that purpose. these programs consider mainly length of the loop between helices, sequence content and either free-energy associated to base stacking […]


Predicting Helical Topologies in RNA Junctions as Tree Graphs

PLoS One
PMCID: 3753280
PMID: 23991010
DOI: 10.1371/journal.pone.0071947

[…] our new module denoted rnajag (rna-junction-as-graph) predicts tree graphs of rna junctions for a given secondary structure (see for the computational procedure). it expands upon our program junction-explorer in several important ways; first, rnajag generates a candidate junction graph model with specific helical arrangements (on top of family type/stacking orientation); second, […]


Candidate RNA structures for domain 3 of the foot and mouth disease virus internal ribosome entry site

Nucleic Acids Res
PMCID: 3561949
PMID: 23275533
DOI: 10.1093/nar/gks1302

[…] cannot predict multiple rna junction structures well, though there are many useful 3d prediction programs as recently surveyed (,). very recently, our rna junction structure prediction program junction-explorer, based on data mining and bioinformatics, was shown to predict the topology of individual rna junction domains with ∼70% or more prediction accuracy (). here, to construct plausible […]

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Junction-Explorer institution(s)
Department of Chemistry, Courant Institute of Mathematical Sciences, New York University, NY, USA; Bioinformatics Program and Department of Computer Science, NJ, USA
Junction-Explorer funding source(s)
This project was funded by the National Science Foundation (EMT award CCF-0727001, grant IIS-0707571) and the National Institutes of Health (grant R01-GM081410).

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