10.1371/journal.pone.0137859.g005
Juan Antonio Garcia-Martin
Juan
Antonio Garcia-Martin
Peter Clote
Peter
Clote
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.
Public Library of Science
2015
estimate rule probabilities
heat shock gene expression
UV absorption experiments
derivational entropy
hiv
scfg
RNA Thermodynamic Structural Entropy Conformational entropy
Turner energy model
hammerhead ribozyme cleavage activity
2015-11-10 03:10:36
Figure
https://plos.figshare.com/articles/figure/_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_/1598571
<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>