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:
Show references
- [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:
Show references
- [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:
Show references
- [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 - predict directly from the pasted sequence:
Submit a new job:
Show references
- [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.
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