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RNAProbe - a web server for normalization and analysis of RNA structure probing data. You can take a (quick) NAP, while we analyze your data :)

NameMethodFilenamesFull string
Demo3_Adenine_Riboswitch_no_ligand_SHAPE_mode_meanAdenine_Riboswitch_Adenine_Riboswitch_no_ligand_QuSHAPE_01_to_Adenine_Riboswitch_no_ligand_QuSHAPE_05_mean_shape_modeGCUUCAUAUAAUCCUAAUGAUAUGGUUUGGGAGUUUCUACCAAGAGCCUUAAACUCUUGAUUAUGAAGUGGCUUCAUAUAAUCCUAAUGAUAUGGUUUGGGAGUUUCUACCAAGAGCCUUAAACUCUUGAUUAUGAAGUG
Demo3_Adenine_Riboswitch_no_ligand_SHAPE_mode_meanAdenine_Riboswitch_Adenine_Riboswitch_no_ligand_QuSHAPE_01_to_Adenine_Riboswitch_no_ligand_QuSHAPE_05_mean_shape_mode0.000.000.000.000.090.020.010.221.000.990.360.050.000.000.000.020.060.210.320.210.080.540.380.400.160.050.010.000.000.000.000.060.090.531.000.320.281.000.360.140.060.020.040.010.030.010.040.091.001.000.320.140.070.020.000.010.020.020.230.550.610.250.110.090.020.070.090.050.020.20
Demo3_Adenine_Riboswitch_no_ligand_SHAPE_mode_meanRNAfold_SHAPEAdenine_Riboswitch_Adenine_Riboswitch_no_ligand_QuSHAPE_01_to_Adenine_Riboswitch_no_ligand_QuSHAPE_05_mean_shape_mode((((((((...((((((.........))))))((....))((((((.......))))))..)))))))).((((((((...((((((.........))))))((....))((((((.......))))))..)))))))).
Demo3_Adenine_Riboswitch_no_ligand_SHAPE_mode_meanShapeKnots_SHAPEAdenine_Riboswitch_Adenine_Riboswitch_no_ligand_QuSHAPE_01_to_Adenine_Riboswitch_no_ligand_QuSHAPE_05_mean_shape_mode((((((((...((((((.........))))))((....))((((((.......))))))..)))))))).((((((((...((((((.........))))))((....))((((((.......))))))..)))))))).
Demo3_Adenine_Riboswitch_no_ligand_SHAPE_mode_meanRNAfold((((((((...((((((.........))))))........((((((.......))))))..)))))))).((((((((...((((((.........))))))........((((((.......))))))..)))))))).
Demo3_Adenine_Riboswitch_no_ligand_SHAPE_mode_meanRNAstructure_ProbKnot((((((((...(((((((......).))))))........((((((.......))))))..)))))))).((((((((...(((((((......).))))))........((((((.......))))))..)))))))).
Demo3_Adenine_Riboswitch_no_ligand_SHAPE_mode_meanRNAstructure_Fold((((((((...((((((.........))))))........((((((.......))))))..)))))))).((((((((...((((((.........))))))........((((((.......))))))..)))))))).
Demo3_Adenine_Riboswitch_no_ligand_SHAPE_mode_meanCentroidFold((((((((....(((((.........))))).........((((((.......))))))..)))))))).((((((((....(((((.........))))).........((((((.......))))))..)))))))).
Demo3_Adenine_Riboswitch_no_ligand_SHAPE_mode_meanCONTRAfold((((((((..((((((((......).))))))((....))((((((.......)))))).))))))))).((((((((..((((((((......).))))))((....))((((((.......)))))).))))))))).
Demo3_Adenine_Riboswitch_no_ligand_SHAPE_mode_meanIPknot((((((((....(((((.........))))).........((((((.......))))))..)))))))).((((((((....(((((.........))))).........((((((.......))))))..)))))))).
Demo3_Adenine_Riboswitch_no_ligand_SHAPE_mode_meanLinearfold_C((((((((...((((((.........))))))........((((((.......))))))..)))))))).((((((((...((((((.........))))))........((((((.......))))))..)))))))).
Demo3_Adenine_Riboswitch_no_ligand_SHAPE_mode_meanLinearfold_V((((((((...((((((.........))))))........((((((.......))))))..)))))))).((((((((...((((((.........))))))........((((((.......))))))..)))))))).
Demo3_Adenine_Riboswitch_no_ligand_SHAPE_mode_meanConsensus_from_predictions((((((((...((((((.........))))))........((((((.......))))))..)))))))).((((((((...((((((.........))))))........((((((.......))))))..)))))))).



Barplot with normalized reactivities

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Heatmap with normalized reactivities

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Secondary structure predictions

RNAfold predicted structure, based on SHAPE reactivities:

RNAfold predicted structure, based on SHAPE reactivities - radiate representation:

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ShapeKnots predicted structure, based on SHAPE reactivities:

ShapeKnots predicted structure, based on SHAPE reactivities - radiate representation:

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RNAfold predicted structure, based on SHAPE reactivities - circular representation:

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ShapeKnots predicted structure, based on SHAPE reactivities - circular representation:

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RNAfold predicted structure, based on SHAPE reactivities - linear representation:

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ShapeKnots predicted structure, based on SHAPE reactivities - linear representation:

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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 )

Analysis mode: shape; outfilename core: Adenine_Riboswitch_Adenine_Riboswitch_no_ligand_QuSHAPE_01_to_Adenine_Riboswitch_no_ligand_QuSHAPE_05_mean_shape_mode.