Experiment-Assisted Secondary Structure Prediction with RNAstructure.
Experimental probing data can be used to improve the accuracy of RNA secondary structure prediction. The software package RNAstructure can take advantage of enzymatic cleavage data, FMN cleavage data, traditional chemical modification reactivity data, and SHAPE reactivity data for secondary structure modeling. This chapter provides protocols for using experimental probing data with RNAstructure to restrain or constrain RNA secondary structure prediction.
Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA.|Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA.
Zhenjiang Zech
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Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA. David_Mathews@urmc.rochester.edu.|Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA. David_Mathews@urmc.rochester.edu.|Department of Biostatistics & Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA. David_Mathews@urmc.rochester.edu.
David H
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Mathews
D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012984:Software; D013816:Thermodynamics; D014584:User-Computer Interface; D064878:Web Browser
D012313:RNA
Chemical modification data; RNA structure prediction; SHAPE; Thermodynamics