Figure 11.

Pseudocode for RNAborMEAalgorithm. Given RNA sequence s = s1, .. ., sn of length n, initial secondary structure S0 of s, RNAborMEA computes for all values of 0 ≤ k n that structure S with base pair distance k from S0, which maximizes the value <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/S5/S6/mathml/M56','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/S5/S6/mathml/M56">View MathML</a>. The pseudocode actually computes only values M(i, j, k) for all i, j, k; the MEA structures are obtained by backtracing. This algorithm clearly runs in O(n3) time with O(n3) space.

Clote et al. BMC Bioinformatics 2012 13(Suppl 5):S6   doi:10.1186/1471-2105-13-S5-S6