Figure 1.

Output of RNAboron the 27 nt bistable switch with nucleotide sequence CUUAUGAGGG UACUCAUAAG AGUAUCC and initial structure S0, the minimum free energy (MFE) structure....... ((((((((....)))))))) with free energy -10.3 kcal/mol. The 16-neighbor of S0 is the metastable structure ((((((((....))))))))....... with free energy -9.9 kcal/mol. The MFE structure appears above the leftmost peak, while the MFE(16) structure appears above the rightmost peak. The output of RNAbor includes a graph of the Boltzmann probabilities <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/S5/S6/mathml/M52','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/S5/S6/mathml/M52">View MathML</a>, and MFE(k) structures, for all 0 ≤ k ≤ 2n. The existence of distinct 'peaks' suggests the presence of a conformational switch.

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