Fig. 4.

Joint secondary structure of the sRNA MicA and the mRNA ompA. The alignment shows the two input alignments concatenated by the linker symbol ‘&’, the joint structure predicted by PETcofold (with parameters δ = 0.9, γ = 0.1 and option -noLP) and the model of the MicA–ompA complex proposed by Udekwu et al. (2005). Sequences are labelled with the genome accession numbers of the corresponding organisms. Angle brackets indicate inter-molecular base pairs. Round and square brackets indicate intra-molecular base pairs. Square brackets indicate positions that are constrained in step 1 of the PETcofold pipeline. For ompA, only 40 nt upstream of the interaction site are shown. The alignment was visualized with Jalview (Waterhouse et al., 2009).