... RNAs (miRNAs/siR-NAs) are very short and have full sequence complemen-tarity to the targets. However some of the regulatoryantisense RNAs are relatively long and are not fullycomplementary ... usesecondary structure prediction methods that do not allow pseudoknots, they fail to predict joint structuresformed by non-trivial interactions between a pair ofRNAs.Another set of methods ... strand is denoted by [i, j]. We denote a base pairbetween the nucleotides i and j by i·j. MFE(i, j) denotesthe minimum free energy structure of [i, j], and MFE(iR,jR, iS, jS) denotes the...