Average values for the run time and the entropy values for 100 random RNA sequences of length n, each having expected compositional frequency of 0:25 for A,C,G,U, where n ranges from 20 to 500 with increments of 5 for conformational entropy.
(A) Average run times as a function of sequence length, where error bars represent ±1 standard deviation. Methods used: DP, FTD, FTD*, ViennaRNA, ViennaRNA*. For random RNAs of length 500 nt, Vienna RNA Package is about three times faster than our code. (B) Standard deviation of the entropy values computed for 100 random RNA, displayed as a function of sequence length. From top to bottom, the first three curves represent uncentered ViennaRNA with ΔT = 10−4, centered ViennaRNA* with ΔT = 10−4, and DP. The bottom curve represents centered FTD with ΔT = 10−4, centered FTD* with ΔT = 10−2, uncentered ViennaRNA with ΔT = 10−2, centered ViennaRNA* with ΔT = 10−2. The average entropy values computed by FTD, FTD*, ViennaRNA, and ViennaRNA* are indistinguishable and since FTD values are shown in the right panel of Fig 1, they are not shown here.