Sequences

Performance of RNAiFold 2.0 vs 1.0
run times are given in seconds
(100 runs per structure, time limit set to 10 minutes)

Modena structures - Dataset A

RNA-CPdesignRNA-LNSdesign
RNAiFold 2.0RNAiFold 1.0RNAiFold 2.0RNAiFold 1.0
IdSizeSolvedAvg. TimeSolvedAvg. TimeSolvedAvg. TimeSolvedAvg. Time
RF00001.1211171003.855761.8701003.4221005.648
RF00002.2151360.013420.77910049.37210024.206
RF00003.9416150.0010-95135.4390-
RF00004.126193960.011990.3201000.0121000.325
RF00005.174520.000824.6059914.5831001.632
RF00006.189940.001930.0691001.8651000.941
RF00007.20154831.409832.0211006.2441006.602
RF00008.1154637.944880.0231006.8871001.844
RF00009.115348421.7517113.33910022.30410030.015
RF00010.2533570-0-0-0-
RF00011.183820-0-0-0-
RF00012.15215960.0251000.7541002.7911000.976
RF00013.1391851000.031990.3441000.0291000.345
RF00014.2871000.0001000.054100-1000.053
RF00015.101140810.328680.4481005.5771003.697
RF00016.15-0-0-0-0-
RF00017.903011000.746847.7361001.45010016.468
RF00018.2-0-0-0-0-
RF00019.115831000.0001000.0671000.7931000.099
RF00020.107-0-0-0-0-
RF00021.101181003.333990.6341000.7741000.148
RF00022.1148700.111925.1591007.4361002.045
RF00024.16-0-0-0-0-
RF00025.122101000.038980.4761000.0361001.120
RF00026.11021000.00010034.778100-990.965
RF00027.7791000.0121000.041982.0251000.048
RF00028.1344630.105370.94610018.29010042.137
RF00029.10773980.220821.8241000.1751000.763
RF00030.30340970.248932.1191002.7461003.261

RNA-SSD structures - Dataset B

RNA-CPdesignRNA-LNSdesign
RNAiFold 2.0RNAiFold 1.0RNAiFold 2.0RNAiFold 1.0
AccessionSizeSolvedAvg. TimeSolvedAvg. TimeSolvedAvg. TimeSolvedAvg. Time
Z83250260841.1149310.3441002.9671004.184
L119352641005.468832.8551000.740996.806
LIU92530289792.199753.964994.98910011.762
U84629299793.3747919.8851009.81610013.137
AF107506337515.9937315.30510022.8739926.504
AF106618350637.638779.16710014.8619964.568
AJ011149376440.8303920.08110031.0690-
S708383899425.6868628.9139930.0629951.020
U63350418682.228778.44110011.3199914.410
AF141485473300.4095021.13510027.47810054.208
U817714910-0-0-0-
AJ1307795066113.9695591.22210021.23110055.622
AF0968366465646.9838116.6800-10026.730
X61771659169.052193.88410058.89182140.392
AJ2364557510-0-0-0-
AJ132572780424.3883832.73610040.34295135.200
AB0158278564412.5631311.58010020.89840105.661
D387778580-0-0-0-
AF02919510534519.0433252.32210060.0790-
X8194912001819.1422950.10595105.6670-
AJ133622129678274.9891142.035522.8120-
AF0569381398543.7464079.96310021.2900-
X9967614420-0-0-0-
L7711714750-0-0-0-

RNA-SSD - Dataset C

RNA-CPdesignRNA-LNSdesign
RNAiFold 2.0RNAiFold 1.0RNAiFold 2.0RNAiFold 1.0
IdSizeSolvedAvg. TimeSolvedAvg. TimeSolvedAvg. TimeSolvedAvg. Time
1651000.0431002.6251000.5581000.137
27910032.8091000.0421000.306990.043
31221000.019930.6191000.0581001.020
41661000.033980.3321000.041000.581
51800-0-0-0-
631470.004451.26410020.0079928.023
7340795.177893.6441008.2531007.335
8372920.082912.4301000.5551009.245
93760-0-0-0-
105836110.861789.62010014.53110031.611


Performance of RNAiFold 1.0 vs other inverse folding methods

Times for Modena structures - Dataset A

Id Size CPdesign Info-RNA Modena RNA-SSD RNAinverse Str. Seq. Img.
RF00001.121 117 21.5 0.0 36.8 1.0 233.1
RF00002.2 151 29.5 62.6 39.4 12.2 -
RF00003.94 161 - 72.1 70.2 - -
RF00004.126 193 1.5 0.1 52.9 2.0 48.3
RF00005.1 74 0.2 0.0 12.4 0.1 0.1
RF00006.1 89 0.3 0.0 15.1 0.6 4.3
RF00007.20 154 5.6 0.0 44.4 1.1 12.4
RF00008.11 54 0.1 0.0 8.7 0.0 0.0
RF00009.115 348 20.8 - 214.1 48.2 -
RF00010.253 357 - - - - -
RF00011.18 382 - - - - -
RF00012.15 215 2.7 25.0 64.5 28.8 139.4
RF00013.139 185 1.6 0.8 51.5 2.8 19.8
RF00014.2 87 0.3 0.0 17.5 0.1 0.0
RF00015.101 140 1.3 0.2 29.1 0.6 52.4
RF00016.15 129 - - - - -
RF00017.90 301 19.3 0.0 208.1 7.0 10.0
RF00018.2 360 12.1 697.0 331.5 - -
RF00019.115 83 0.2 0.0 14.9 0.2 0.3
RF00020.107 119 - - - - -
RF00021.10 118 0.3 0.0 27.8 0.2 0.2
RF00022.1 148 0.7 0.0 32.6 0.9 225.5
RF00024.16 451 - - - - -
RF00025.12 210 1.4 47.9 54.2 2.9 -
RF00026.1 102 0.4 5.5 15.2 1.4 173.2
RF00027.7 79 0.1 0.0 17.4 0.1 0.4
RF00028.1 344 6.2 - - 71.2 -
RF00029.107 73 0.3 0.0 10.4 0.2 0.3
RF00030.30 340 6.8 57.3 186.8 39.3 -


Times for RNA-SSD structures - Dataset B

Accesion Size CPdesign Info-RNA Modena RNA-SSD RNAinverse Str. Seq. Img.
Z83250 260 2.6 0.0 125.6 2.1 213.9
L11935 264 5.0 0.0 121.8 1.1 109.1
LIU92530 289 10.0 0.0 - 354.9 351.9
U84629 299 5.5 0.0 153.1 6.4 554.6
AF107506 337 9.5 0.0 218.2 6.6 347.6
AF106618 350 20.8 0.0 131.9 2.1 265
AJ011149 376 140.5 0.0 - 62.5 463.5
S70838 389 27.9 0.0 275.4 7.1 295.2
U63350 418 11.7 1.2 191.3 2.8 346.3
AF141485 473 51.4 0.1 266.6 65.1 -
U81771 491 28.8 0.1 221.6 26.2 -
AJ130779 506 70.1 0.1 227 11 507.2
AF096836 646 48.2 0.3 440.4 15.5 -
X61771 659 67.0 0.3 - 129.6 -
AJ236455 751 - - - 39.2 -
AJ132572 780 158.2 0.3 - 30 -
AB015827 856 245.2 5.2 - 49.7 -
D38777 858 173.3 1.5 - 17.3 -
AF029195 1053 321.0 2.7 - 42.2 -
X81949 1200 197.1 15.7 - 48.5 -
AJ133622 1296 - 7.8 - 128.6 -
AF056938 1398 477.9 2.5 319.7 58.5 -
X99676 1442 569.2 9.8 510.1 156.5 -
L77117 1475 - 20.4 - 90.4 -


Times for RNA-SSD - Dataset C

Id Size CPdesign Info-RNA Modena RNA-SSD RNAinverse Structure Sequence Img.
1 65 0.1 0.0 19.3 0.1 0.1
2 79 0.0 0.0 26.2 0.1 0.1
3 122 2.7 0.0 69.4 1.5 4.1
4 167 0.7 0.0 104.5 0.9 4.1
5 180 0.7 165.7 245.7 - 407.9
6 314 6.2 0.8 192.2 0.0 362
7 340 9.8 0.8 405.9 12.8 254.6
8 372 7.0 19.5 421.1 48.4 -
9 376 - - - - -
10 583 32.9 0.1 397.2 6.9 287.6

EteRNA structures

Name Restrictions Size Time Structure Sequence Image
Prion Pseudoknot View 36 16.29
Human astrovirus View 43 419.69
Homo Sapiens 1 Series View 83 4.19
HIV Primer Binding Site View 107 482.67
Homo Sapiens 3 View 109 126.22
Other Ribosomal RNA View 112 11.35
Bacilus Subtilis sRNA View 113 577.50
5s Ribosomal RNA View 120 126.44
Tribolium Castaneum View 123 50.17
Oryza sativa 4 View 176 187.03
Symbiotic plasmid View 300 479.35
Telomerase RNA View 546 441.70