Figure 3.
Illustration of the four cases in Equation (6). A) NE(i, j) equals NE(i, j−1) which is the total normalized energy of all loops in the optimal secondary structure R[i, j − 1] of subsequence S[i, j − 1]. B) NE(i, j) equals NE(i + 1, j) which is the total normalized energy of all loops in the optimal secondary structure R[i + 1, j] of subsequence S[i + 1, j]. C) NE(i, j) equals NEP(i, j) which is the total normalized energy of all loops in the optimal secondary structure R[i, j] of subsequence S[i, j], where S[i] and S[j] form a base pair. D) NE(i, j) equals the minimum of NE(i, k − 1) plus NE(k, j) for all i < k < j. The dashed line between two nucleotides means that the two nucleotides may or may not form a base pair. The solid line between two nucleotides means that the two nucleotides form a base pair.