Not very nice logo, but the first author insisted on it. The last author thinks it could be much better. Or the pure text instead.

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

Analysis mode:

Normalization, prediction of secondary structure and visualization of SHAPE experiment [1] [2] results after QuShape analysis. The pipeline involves the standard normalization protocol [3], and allows for prediction and visualization of studied RNA secondary structure. The SHAPE-directed predictions are generated by RNAfold [4] and ShapeKnots [5].

Examples:

Adenine riboswitch without ligand, single QuShape analysis:

Adenine riboswitch with a ligand (adenine), single QuShape analysis:

Adenine riboswitch, multiple QuShape analysis files, mean calculated from all repetitions:

Adenine riboswitch with the use of user-provided, normalized reactivities:

Submit a new job:


Submit a file with the sequence. See FAQ for supported file extensions. Length of 2-600 nt supported.
Paste a sequence - just a sequence or in full fasta format. See FAQ for examples. Length of 2-600 nt supported.
File(s) containing QuShape results (output of QuSHAPe program). For replicates, submit multiple files. See FAQ for supported file extensions.
File containing normalized reactivity data. See FAQ for supported file extensions.
Optional settings:
Submit a file with the secondary structure in dot-bracket notation. See FAQ for examples and supported file extensions.
Paste a secondary structure in dot-bracket notation. See FAQ for examples.
Submit a pdb file with the RNA structure. The reactivities will be mapped to this three-dimensional structure.
Paste a pdb file with the RNA structure.
Default=0
Default=0
which color do you like most?
  • [1] Merino, E.J., Wilkinson, K.A., Coughlan, J.L. and Weeks, K.M., 2005. RNA structure analysis at single nucleotide resolution by selective 2 ‘-hydroxyl acylation and primer extension (SHAPE). Journal of the American Chemical Society, 127(12), pp.4223-4231.
  • [2] Wilkinson, K.A., Merino, E.J. and Weeks, K.M., 2006. Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nature protocols, 1(3), p.1610.
  • [3] Karabiber, F., McGinnis, J.L., Favorov, O.V. and Weeks, K.M., 2013. QuShape: rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis. Rna, 19(1), pp.63-73.
  • [4] Lorenz, R., Bernhart, S.H., Zu Siederdissen, C.H., Tafer, H., Flamm, C., Stadler, P.F. and Hofacker, I.L., 2011. ViennaRNA Package 2.0. Algorithms for molecular biology, 6(1), p.26.
  • [5] Reuter, J.S. and Mathews, D.H., 2010. RNAstructure: software for RNA secondary structure prediction and analysis. BMC bioinformatics, 11(1), p.129.

Normalization, prediction of secondary structure and visualization of DMS probing experiment [1] [2] [3], after QuShape analysis. The pipeline involves the SHAPE normalization protocol [4], and allows for prediction and visualization of studied RNA secondary structure. The DMS-directed predictions are generated by Fold [5].

Examples:

Adenine riboswitch - DMS probing, three QuShape analysis files:

Adenine riboswitch - DMS probing, three QuShape analysis files, greying-out turned off:

Submit a new job:


Submit a file with the sequence. See FAQ for supported file extensions. Length of 2-600 nt supported.
Paste a sequence - just a sequence or in full fasta format. See FAQ for examples. Length of 2-600 nt supported.
File(s) containing QuShape results (output of QuSHAPe program). For replicates, submit multiple files. See FAQ for supported file extensions.
File containing normalized reactivity data. See FAQ for supported file extensions.
Optional settings:
Submit a file with the secondary structure in dot-bracket notation. See FAQ for examples and supported file extensions.
Paste a secondary structure in dot-bracket notation. See FAQ for examples.
Submit a pdb file with the RNA structure. The reactivities will be mapped to this three-dimensional structure.
Paste a pdb file with the RNA structure.
Default=0
Default=0
which color do you like most?
  • [1] Stern, S., Moazed, D. and Noller, H.F., 1988. [33] Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. In Methods in enzymology (Vol. 164, pp. 481-489). Academic Press.
  • [2] Peattie, D.A. and Gilbert, W., 1980. Chemical probes for higher-order structure in RNA. Proceedings of the National Academy of Sciences, 77(8), pp.4679-4682.
  • [3] Harris, K.A., Crothers, D.M. and Ullu, E.L.I.S.A.B.E.T.T.A., 1995. In vivo structural analysis of spliced leader RNAs in Trypanosoma brucei and Leptomonas collosoma: a flexible structure that is independent of cap4 methylations. RNA, 1(4), pp.351-362.
  • [4] Karabiber, F., McGinnis, J.L., Favorov, O.V. and Weeks, K.M., 2013. QuShape: rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis. Rna, 19(1), pp.63-73.
  • [5] Reuter, J.S. and Mathews, D.H., 2010. RNAstructure: software for RNA secondary structure prediction and analysis. BMC bioinformatics, 11(1), p.129.

Normalization, prediction of secondary structure and visualization of CMCT probing experiment [1] [2] [3], after QuShape analysis. The pipeline involves the SHAPE normalization protocol [4], and allows for prediction and visualization of studied RNA secondary structure. The CMCT-directed predictions are generated by Fold [5].

Examples:

Adenine riboswitch - CMCT probing, three QuShape analysis files:

Adenine riboswitch - CMCT probing, three QuShape analysis files, user-provided secondary structure:

Submit a new job:


Submit a file with the sequence. See FAQ for supported file extensions. Length of 2-600 nt supported.
Paste a sequence - just a sequence or in full fasta format. See FAQ for examples. Length of 2-600 nt supported.
File(s) containing QuShape results (output of QuSHAPe program). For replicates, submit multiple files. See FAQ for supported file extensions.
File containing normalized reactivity data. See FAQ for supported file extensions.
Optional settings:
Submit a file with the secondary structure in dot-bracket notation. See FAQ for examples and supported file extensions.
Paste a secondary structure in dot-bracket notation. See FAQ for examples.
Submit a pdb file with the RNA structure. The reactivities will be mapped to this three-dimensional structure.
Paste a pdb file with the RNA structure.
Default=0
Default=0
which color do you like most?
  • [1] Stern, S., Moazed, D. and Noller, H.F., 1988. [33] Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. In Methods in enzymology (Vol. 164, pp. 481-489). Academic Press.
  • [2] Peattie, D.A. and Gilbert, W., 1980. Chemical probes for higher-order structure in RNA. Proceedings of the National Academy of Sciences, 77(8), pp.4679-4682.
  • [3] Harris, K.A., Crothers, D.M. and Ullu, E.L.I.S.A.B.E.T.T.A., 1995. In vivo structural analysis of spliced leader RNAs in Trypanosoma brucei and Leptomonas collosoma: a flexible structure that is independent of cap4 methylations. RNA, 1(4), pp.351-362.
  • [4] Karabiber, F., McGinnis, J.L., Favorov, O.V. and Weeks, K.M., 2013. QuShape: rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis. Rna, 19(1), pp.63-73.
  • [5] Reuter, J.S. and Mathews, D.H., 2010. RNAstructure: software for RNA secondary structure prediction and analysis. BMC bioinformatics, 11(1), p.129.

Prediction of the secondary structure of RNA, using various prediction methods, and visualization of the consensus structure from predictions.

Examples:

Adenine riboswitch:

Adenine riboswitch - predict directly from the pasted sequence:

Submit a new job:


Submit a file with the sequence. See FAQ for supported file extensions. Length of 2-600 nt supported
Paste a sequence - just a sequence or in full fasta format. See FAQ for examples. Length of 2-600 nt supported

  • [1] Merino, E.J., Wilkinson, K.A., Coughlan, J.L. and Weeks, K.M., 2005. RNA structure analysis at single nucleotide resolution by selective 2 ‘-hydroxyl acylation and primer extension (SHAPE). Journal of the American Chemical Society, 127(12), pp.4223-4231.
  • [2] Wilkinson, K.A., Merino, E.J. and Weeks, K.M., 2006. Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nature protocols, 1(3), p.1610.
  • [3] Karabiber, F., McGinnis, J.L., Favorov, O.V. and Weeks, K.M., 2013. QuShape: rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis. Rna, 19(1), pp.63-73.

Number of jobs in queue: 0 (Thu Aug 14 18:57:05 UTC 2025); 8126 jobs submitted so far.