Average values for the run time and the entropy values for 100 random RNA sequences of length <i>n</i>, each having expected compositional frequency of 0:25 for A,C,G,U, where <i>n</i> ranges from 20 to 500 with increments of 5 for conformational entropy.
Antonio Garcia-MartinJuan
ClotePeter
2015
<p><i>(A)</i> 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. <i>(B)</i> 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 Δ<i>T</i> = 10<sup>−4</sup>, centered ViennaRNA* with Δ<i>T</i> = 10<sup>−4</sup>, and DP. The bottom curve represents centered FTD with Δ<i>T</i> = 10<sup>−4</sup>, centered FTD* with Δ<i>T</i> = 10<sup>−2</sup>, uncentered ViennaRNA with Δ<i>T</i> = 10<sup>−2</sup>, centered ViennaRNA* with Δ<i>T</i> = 10<sup>−2</sup>. The average entropy values computed by FTD, FTD*, ViennaRNA, and ViennaRNA* are indistinguishable and since FTD values are shown in the right panel of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0137859#pone.0137859.g001" target="_blank">Fig 1</a>, they are not shown here.</p>