Fig. 1.

A schematic diagram of DotcodeR. Potential structured RNA genes are assumed to be taken from the sliding windows in two genomic sequences, which are shown as gray rectangles. In this figure the windows are drawn to be non-overlapping but in reality adjacent windows overlap. All windows from one sequence are compared to all windows from the other sequence as indicated by the thin blue lines. For these sequence windows, the secondary structure dot plots are computed using the partition function-based method. Coarse-grained dot plots (binary vectors) are then obtained by the conversion rule stated in the main text. Finally, a structural similarity score can be calculated by dot product between two binary vectors