The SHAPE values do not have to be in the range between 0 and 1. They can be larger than 1. SHAPE reactivity normalization is usually done in the SHAPE experiments to remove the outliers and normalize the reactivity values into a range. If the SHAPE values have not been normalized, we recommend the users to use software shapemapper to run the normalization such that “reactivities are normalized by dividing by the mean reactivity of the top 10% of reactivities after reactivities above a threshold are excluded.” The details can be found at and in the paper: Low, J. T., & Weeks, K. M. (2010). SHAPE-directed RNA secondary structure prediction. Methods, 52(2), 150-158.

SHAPE file format

Users can provide SHAPE experimental information to help 2D structure prediction. The SHAPE file contains two columns. The first column corresponds to the nucleotide index, and the second column corresponds to the SHAPE reactivity. You can only keep the nucleotides having SHAPE values and skip those not having SHAPE values. An example is shown below.

1 0.2
2 0.1
3 0.15
10 0.8
25 0.1