Figure 2.

Boltzmann density plot for RNAbor, along with approximating relative frequency plots for RNAborMEAandRNAlocoptfor the 101 nt RNA sequence UACUUAUCAA GAGAGGUGGA GGGACUGGCC CGCUGAAACC UCAGCAACAG AACGCAUCUG UCUGUGCUAA AUCCUGCAAG CAAUAGCUUG AAAGAUAAGU U for the SAM riboswitch aptamter with GenBank accession code AP004597.1/118941-119041. The program RNAbor computes the Boltzmann probability <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/S5/S6/mathml/M53','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/S5/S6/mathml/M53">View MathML</a>, where <a onClick="popup('http://www.biomedcentral.com/1471-2105/13/S5/S6/mathml/M54','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/13/S5/S6/mathml/M54">View MathML</a>, where S0 is the initial structure (taken as the minimum free energy here). The script RNAbor-Sample calls Sfold on 1000 structures, in order to compute a relative frequence fk pk of all k-neighbors of S0. Finally, we compute relative frequency of RNAlocopt[34], a program that samples only locally optimal secondary structures, having the property that one cannot obtain a lower energy structure by adding or removing a single base pair.

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