Table 5.
Comparison of Iterative HFold F-measure with ShapeKnots on SHAPE data
|
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 |