Figure 4

Joint secondary structure prediction of the sRNA OxyS and its target mRNA fhlA. The sequence alignment shows the two input alignments concatenated by the linker symbol "&", the joint secondary structure predicted by our algorithm (with δ = 0.9 and γ = 0.1 and disallowing base pairs that only occur isolated in the thermodynamic part) and the interaction model of OxyS-fhlA [11]. The prediction was performed (a) without and (b) with extension of the constrained stems. Angle brackets indicate inter-molecular base pairs between the two RNAs. Round and square brackets indicate intra-molecular base pairs. Square brackets indicate base pairs of the partial structure σ^p. Shown are all columns with < 75% gaps. Jalview [33] was used for alignment visualisation.