From: A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures
Training set | Len | PK | Iter. HFold | ShapeKnots | ||||
---|---|---|---|---|---|---|---|---|
 |  |  | sen | ppv | F | sen | ppv | F |
Pre-Q1 riboswitch, B. subtilis | 34 | 1 | 62.5 | 100 | 76.9 | 100 | 100 | 100 |
Telomerase pseudoknot, human | 47 | 1 | 100 | 100 | 100 | 100 | 100 | 100 |
tRNA(asp), yeast | 75 | 0 | 81.0 | 100 | 89.5 | 95.2 | 95.2 | 95.2 |
TPP riboswitch, E. coli | 79 | 0 | 46.5 | 47.6 | 47.1 | 95.4 | 87.5 | 91.3 |
SARS corona virus pseudoknot | 82 | 1 | 69.2 | 86.3 | 69.2 | 84.6 | 88.0 | 86.3 |
cyclic-di-GMP riboswitch, V. cholerae | 97 | 0 | 85.5 | 81.0 | 83.2 | 89.3 | 86.2 | 87.7 |
SAM I riboswitch, T. tengcongenis | 118 | 1 | 79.5 | 91.2 | 84.9 | 92.3 | 97.3 | 94.7 |
M-Box riboswitch, B. subtilis | 154 | 0 | 87.5 | 91.3 | 89.4 | 87.5 | 91.3 | 89.3 |
P546 domain, bI3 group I intron | 155 | 0 | 55.4 | 57.4 | 56.4 | 94.6 | 96.4 | 95.5 |
Lysine riboswitch, T. maritima | 174 | 1 | 85.7 | 94.7 | 90.0 | 87.3 | 88.7 | 88.0 |
Group I intron, Azoarcus sp. | 214 | 1 | 52.4 | 54.1 | 53.2 | 92.1 | 95.1 | 93.5 |
Signal recognition particle RNA, human | 301 | 0 | 70.0 | 73.7 | 71.8 | 55.0 | 53.9 | 54.4 |
Hepatitis C virus IRES domain | 336 | 1 | 71.2 | 74.0 | 72.5 | 92.3 | 96.0 | 94.1 |
RNase P, B. subtilis | 405 | 1 | 55.7 | 59.3 | 57.4 | 75.6 | 79.8 | 77.7 |
Group II intron, O. iheyensis | 412 | 1 | 87.9 | 95.9 | 91.7 | 93.2 | 97.6 | 95.3 |
Group I intron, T. thermophila | 425 | 1 | 83.2 | 85.2 | 84.2 | 93.9 | 91.2 | 92.5 |
5’ domain of 23S rRNA, E. coli | 511 | 0 | 84.0 | 72.5 | 77.8 | 92.4 | 76.4 | 83.6 |
5’ domain of 16S rRNA, E. coli | 530 | 0 | 73.6 | 69.0 | 71.2 | 89.9 | 80.6 | 84.9 |
Test set | Len | PK | Iter. HFold | ShapeKnots | ||||
 |  |  | sen | ppv | F | sen | ppv | F |
Fluoride riboswitch, P. syringae | 66 | 1 | 100 | 100 | 100 | 93.7 | 93.7 | 93.7 |
Adenine riboswitch, V. vulnificus | 71 | 0 | 100 | 100 | 100 | 100 | 100 | 100 |
tRNA(phe), E. coli | 76 | 0 | 100 | 100 | 100 | 100 | 84.0 | 91.3 |
5S rRNA, E. coli | 120 | 0 | 91.4 | 91.4 | 91.4 | 85.7 | 76.9 | 81.1 |
5’ domain of 16S rRNA, H. volcanii | 473 | 0 | 90.3 | 82.3 | 86.1 | 89.6 | 82.7 | 86.0 |
HIV-1 5’ pseudoknot domain | 500 | 1 | 45.4 | 50.4 | 47.7 | 100 | 100 | 100 |