Overview of a complete hSHAPE experiment, processed using ShapeFinder and representing a total read length of 415 nt from an HIV-1 transcript RNA. (A) Raw electropherogram from a DNA sequencer. The data consist of four channels of fluorescence intensity information as a function of elution time. (B) Preprocessed SHAPE data. Each channel now represents dye amount, not fluorescence, as a function of elution time for each of the four channels. For clarity, A and C sequencing ladders are offset from the (+) and (−) reagent channels. (C) Sequence alignment and whole-channel Gaussian peak integration using the Align and Integrate tool to calculate absolute SHAPE reactivities.
