REEFFIT Documentation¶

REEFFIT (RNA Ensemble Extraction From Footprinting Instights Tool) is a method to fit RNA secondary structure ensembles to multi-dimensional chemical mapping (MCM) data. Currently, the method can take data from multiple mutate-and-map or mutate-bind-and-map (mutate-and-map plus ligand titrations, e.g. for riboswitches) experiments. Output is a set of weights and expected reactivities for each structure that linearly combine to form the data. If the structural ensemble is not provided, REEFFIT uses RNAstructure to generate a suboptimal set of structures of all mutants.