Table 2.
Comparison of RNA-ensign (columns A) with multiple runs of RNAinverse (C) and NUPACK (D)
| Length | Probability |
Entropy |
Time (s) |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A | B | C | D | A | B | C | D | A | B | C | D | |
| 0–40 | 0.69 | 0.65 | 0.60 | 0.97 | 0.056 | 0.051 | 0.065 | 0.003 | 62 | 28 | 61 | 27 |
| 41–80 | 0.35 | 0.21 | 0.53 | 0.89 | 0.148 | 0.157 | 0.100 | 0.008 | 1883 | 742 | 711 | 8973 |
| 81+ | 0.40 | 0.30 | 0.29 | 0.93 | 0.062 | 0.147 | 0.125 | 0.006 | 9332 | 2434 | 1269 | 2920 |
We ran RNAinverse 10 000 times and NUPACK 100 times on the RNA-STRAND dataset using random seeds (C+G content and A+G content of 50%) and reported the Boltzmann probability of the target structure and the base pair entropy of the best solution found over all runs. The total running time is indicated in seconds in the last columns. We also included the performances achieved by RNA-ensign with a number of mutations bounded by 50% (B) of the number of nucleotides.