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

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