Sample outputs from RNAborMEAon a 143 nt TPP-riboswitch, AF269819/1811-1669 with sequence CUACUAGGGG AGCCAAAAGG CUGAGAUGAA UGUAUUCAGA CCCUUAUAAC CUGAUUUGGU UAAUACCAAC GUAGGAAAGU AGUUAUUAAC UAUUCGUCAU UGAGAUGUCU UGGUCUAACU ACUUUCUUCG CUGGGAAGUA GUU. We took the TPP riboswitch aptamer from the Rfam database , then extracted right-flanking nucleotides from the corresponding EMBL file, in order to include the expression platform. Displayed from left to right are the structures MEA(0) and MEA(61) (the structure MEA(52) is similar to that of MEA(61) and corresponds to a free energy local minimum in the left figure.) The structure MEA(61) had the highest MEA score over all structural neighbors, including the original structure S0 = MEA(0), and had free energy, -46.0 kcal/mol, that was equal to that of the initial structure S0 = MEA(0), which is the minimum free energy structure for the given sequence.
Clote et al. BMC Bioinformatics 2012 13(Suppl 5):S6 doi:10.1186/1471-2105-13-S5-S6