Average values for structural entropy and run time (in seconds) for the 960 transfer RNA sequences from the seed alignment of Rfam family RF00005.

Methods include: DP: dynamic programming algorithm from our program RNAentropy, using the Turner 2004 energy parameters; FTD (ΔT = 10−7): finite difference computation of 〈E〉=RT2·lnZ(T+ΔT)-lnZ(T)ΔT, where formal and table temperature are uncoupled, and formal temperature increment is 10−7; SCFG(G4,Rfam5): SCFG method [24] using grammar G4 with training dataset ‘Rfam5’ SCFG(G5,Rfam5): SCFG method using grammar G5 with training dataset ‘Rfam5’ SCFG(G6,Rfam5): SCFG method using grammar G6 with training dataset ‘Rfam5’. FTD returns very similar values for temperature increments 10−7 ≤ ΔT ≤ 10−11; however, for smaller temperature increments, there is a slight deviation due to numerical precision issues—for example, average entropy of FTD with ΔT = 10−12 is 5.238878±1.504748, with similar run times as other FTD runs.