RNAProbe - a web server for normalization and analysis of RNA structure probing data. You can take a (quick) NAP, while we analyze your data :)
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| Name | Method | Filenames | Full string | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Demo1_Adenine_Riboswitch_no_ligand_SHAPE_mode | Adenine_Riboswitch_Adenine_Riboswitch_no_ligand_QuSHAPE_01_shape_mode | GCUUCAUAUAAUCCUAAUGAUAUGGUUUGGGAGUUUCUACCAAGAGCCUUAAACUCUUGAUUAUGAAGUG | G | C | U | U | C | A | U | A | U | A | A | U | C | C | U | A | A | U | G | A | U | A | U | G | G | U | U | U | G | G | G | A | G | U | U | U | C | U | A | C | C | A | A | G | A | G | C | C | U | U | A | A | A | C | U | C | U | U | G | A | U | U | A | U | G | A | A | G | U | G | |
| Demo1_Adenine_Riboswitch_no_ligand_SHAPE_mode | Adenine_Riboswitch_Adenine_Riboswitch_no_ligand_QuSHAPE_01_shape_mode | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 0.06 | 0.02 | 0.40 | 1.00 | 1.00 | 0.28 | 0.03 | 0.00 | 0.00 | 0.00 | 0.02 | 0.06 | 0.20 | 0.25 | 0.17 | 0.05 | 0.48 | 0.21 | 0.40 | 0.11 | 0.03 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.01 | 0.16 | 0.59 | 1.00 | 0.32 | 0.39 | 1.00 | 0.31 | 0.12 | 0.00 | 0.00 | 0.02 | 0.00 | 0.02 | 0.00 | 0.00 | 0.12 | 1.00 | 1.00 | 0.32 | 0.12 | 0.06 | 0.02 | 0.00 | 0.00 | 0.00 | 0.00 | 0.08 | 0.40 | 0.49 | 0.09 | 0.01 | 0.04 | 0.00 | 0.03 | 0.00 | 0.00 | 0.00 | 0.05 | ||
| Demo1_Adenine_Riboswitch_no_ligand_SHAPE_mode | RNAfold_SHAPE | Adenine_Riboswitch_Adenine_Riboswitch_no_ligand_QuSHAPE_01_shape_mode | ((((((((...((((((.........))))))((....))((((((.......))))))..)))))))). | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | ( | ( | . | . | . | . | ) | ) | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . |
| Demo1_Adenine_Riboswitch_no_ligand_SHAPE_mode | ShapeKnots_SHAPE | Adenine_Riboswitch_Adenine_Riboswitch_no_ligand_QuSHAPE_01_shape_mode | ((((((((...((((((.........))))))........((((((.......))))))..)))))))). | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . |
| Demo1_Adenine_Riboswitch_no_ligand_SHAPE_mode | RNAfold | ((((((((...((((((.........))))))........((((((.......))))))..)))))))). | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . | |
| Demo1_Adenine_Riboswitch_no_ligand_SHAPE_mode | RNAstructure_ProbKnot | ((((((((...(((((((......).))))))........((((((.......))))))..)))))))). | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | ) | . | ) | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . | |
| Demo1_Adenine_Riboswitch_no_ligand_SHAPE_mode | RNAstructure_Fold | ((((((((...((((((.........))))))........((((((.......))))))..)))))))). | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . | |
| Demo1_Adenine_Riboswitch_no_ligand_SHAPE_mode | CentroidFold | ((((((((....(((((.........))))).........((((((.......))))))..)))))))). | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . | |
| Demo1_Adenine_Riboswitch_no_ligand_SHAPE_mode | CONTRAfold | ((((((((..((((((((......).))))))((....))((((((.......)))))).))))))))). | ( | ( | ( | ( | ( | ( | ( | ( | . | . | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | ) | . | ) | ) | ) | ) | ) | ) | ( | ( | . | . | . | . | ) | ) | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | ) | ) | ) | ) | ) | ) | ) | ) | ) | . | |
| Demo1_Adenine_Riboswitch_no_ligand_SHAPE_mode | IPknot | ((((((((....(((((.........))))).........((((((.......))))))..)))))))). | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | . | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . | |
| Demo1_Adenine_Riboswitch_no_ligand_SHAPE_mode | Linearfold_C | ((((((((...((((((.........))))))........((((((.......))))))..)))))))). | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . | |
| Demo1_Adenine_Riboswitch_no_ligand_SHAPE_mode | Linearfold_V | ((((((((...((((((.........))))))........((((((.......))))))..)))))))). | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . | |
| Demo1_Adenine_Riboswitch_no_ligand_SHAPE_mode | Consensus_from_predictions | ((((((((...((((((.........))))))........((((((.......))))))..)))))))). | ( | ( | ( | ( | ( | ( | ( | ( | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | . | . | . | . | . | . | ( | ( | ( | ( | ( | ( | . | . | . | . | . | . | . | ) | ) | ) | ) | ) | ) | . | . | ) | ) | ) | ) | ) | ) | ) | ) | . |
Secondary structure predictions
RNAfold predicted structure, based on SHAPE reactivities:
RNAfold predicted structure, based on SHAPE reactivities - radiate representation:
ShapeKnots predicted structure, based on SHAPE reactivities:
ShapeKnots predicted structure, based on SHAPE reactivities - radiate representation:
RNAfold predicted structure, based on SHAPE reactivities - circular representation:
ShapeKnots predicted structure, based on SHAPE reactivities - circular representation:
RNAfold predicted structure, based on SHAPE reactivities - linear representation:
ShapeKnots predicted structure, based on SHAPE reactivities - linear representation:
Other secondary structure predictions methods and visualisations
Reactivity mapping to structures predicted by other methods are also ready to display or download. Secondary structure to display and copy to clipboard, links to external tools (SimRNAweb )
| method | radiate | circular | line | secondary structure | copy | SimRNAweb |
|---|---|---|---|---|---|---|
| RNAfold | display | | display | | display | | Predict 3D structure for this SS | ||
| ProbKnot | display | | display | | display | | Predict 3D structure for this SS | ||
| Fold | display | | display | | display | | Predict 3D structure for this SS | ||
| CentroidFold | display | | display | | display | | Predict 3D structure for this SS | ||
| CONTRAfold | display | | display | | display | | Predict 3D structure for this SS | ||
| IPknot | display | | display | | display | | Predict 3D structure for this SS | ||
| LinearFold_C | display | | display | | display | | Predict 3D structure for this SS | ||
| LinearFold_V | display | | display | | display | | Predict 3D structure for this SS | ||
| Consensus | display | | display | | display | | Predict 3D structure for this SS |
Tomasz K. Wirecki, Katarzyna Merdas, Agata Bernat, Michał J. Boniecki, Janusz M. Bujnicki, and Filip Stefaniak, RNAProbe - a web server for normalization and analysis of RNA structure probing data. Nucleic Acids Research, Volume 48, Issue W1, 02 July 2020, Pages W292–W299, https://doi.org/10.1093/nar/gkaa396
Analysis mode: shape; outfilename core: Adenine_Riboswitch_Adenine_Riboswitch_no_ligand_QuSHAPE_01_shape_mode.