Table 1 The benchmarking results on the structural alignments of the CMfinder dataset ( β=10)
Family | #seq | MPI | RNAalifold | PhyloRNAalifold | RNAalifold with RIBOSUM | PhyloRNAalifold with RIBOSUM | PETFold |
|---|---|---|---|---|---|---|---|
Cobalamin | 430 | 49.7 | 0.756 | 0.951 | 0.591 | 0.951 | 0.976 |
ctRNA_pGA1 | 15 | 73.0 | 0.979 | 0.979 | 0.979 | 0.979 | 1.000 |
Entero_CRE | 56 | 81.7 | 0.912 | 0.912 | 0.916 | 0.916 | 1.000 |
Entero_OriR | 60 | 87.4 | 0.47 | 0.681 | 0.703 | 0.703 | 0.747 |
glmS | 18 | 57.4 | 0.973 | 0.987 | 1.000 | 1.000 | 0.987 |
Histone3 | 52 | 46.0 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
Intron_gpII | 98 | 52.3 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
IRE | 62 | 76.8 | 0.814 | 0.854 | 0.965 | 0.965 | 0.965 |
let-7 | 67 | 66.4 | 0.861 | 0.967 | 1.000 | 1.000 | 0.915 |
lin-4 | 12 | 68.8 | 0.977 | 1.000 | 1.000 | 1.000 | 0.836 |
Lysine | 47 | 48.4 | 0.952 | 0.981 | 0.981 | 0.981 | 0.952 |
mir-10 | 36 | 67.9 | 0.789 | 0.865 | 0.957 | 0.957 | 0.935 |
Purine | 133 | 54.7 | 0.904 | 1.000 | 1.000 | 1.000 | 0.977 |
RFN | 144 | 68.1 | 0.826 | 0.851 | 0.826 | 1.000 | 1.000 |
Rhino_CRE | 12 | 81.4 | 0.581 | 0.581 | 0.976 | 0.976 | 0.750 |
S_box | 433 | 62.9 | 0.883 | 0.924 | 0.963 | 1.000 | 0.944 |
s2m | 38 | 78.3 | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
SECIS | 61 | 41.0 | 0.972 | 1.000 | 1.000 | 1.000 | 0.972 |
Tymo_tRNA-like | 28 | 68.2 | 0.908 | 0.908 | 0.910 | 0.910 | 0.975 |
| Â | Â | Mean | 0.871 | 0.918 | 0.935 | 0.965 | 0.944 |
| Â | Â | Specificity | 1.000 | 1.000 | 1.000 | 1.000 | 1.000 |
| Â | Â | Sensitivity | 0.802 | 0.881 | 0.919 | 0.952 | 0.922 |