Fig. 2.

Design of RNA-PAIRS network is presented in block form. Blocks with heavier dark outlines represent the more complex portions of the algorithm—both in terms of computational complexity as well as algorithm design. The box for “user input” identifies the current peak list input for the software, which will be extended to include other experimental data. The direction of the arrows identifies the “flow of logic” in the software. The rightmost box (that intersects “curved” arrows) is the portion of the software where probabilities are updated using the “back and forth” (reverberating) iteration