(Left) Pseudo-Boltzmann and uniform probabilities of structural neighbors MEA(k) for the 49 nt SECIS sequence fdhA, with nucleotide sequence CGCCACCCUG CGAACCCAAU AAUAAAAUAU ACAAGGGAGC AAGGUGGCG and where S0 is (((((((.(((...(((.................))).))).))))))). Here, the (formal) parameter RT taken to be 49 (length of sequence), in order to uniformize MEA scores to range between 0 and 1. The pseudo-Boltzmann probability is defined by , where (i) Z(k) = Σexp(MEA(S)/RT), the sum being taken over all S such that dBP(S0, S) = k, and (ii) Z = ΣkZ(k). The uniform probability is defined by , where N(k) is the number of k-neighbors of S0 and N is the total number of secondary structures. (Right) Pseudo-Boltzmann probabilities for MEA(k) structural neighbors of the 27 nt Vienna bistable switch with nucleotide sequence CUUAUGAGGG UACUCAUAAG AGUAUCC and initial (minimum free energy) structure.......((((((((....)))))))). The left curve is when RT = 0.6, the approximate value obtained by multiplying the universal gas constant 0.00198 kcal/mol times 310 Kelvin. In contrast, the right curve is when RT = 27 (length of sequence). Though not shown in this graph, the pseudo-Boltzmann distribution is identical with the uniform distribution, when RT = n, where n is sequence length.
Clote et al. BMC Bioinformatics 2012 13(Suppl 5):S6 doi:10.1186/1471-2105-13-S5-S6