Table 3 RNA FRABASE 2.0, 1.0 and FASTR3D - performance comparison.
Pattern (query) | Description of the query pattern and advanced options (in RNA FRABASE 2.0) | Number of results | ||
|---|---|---|---|---|
| Â | Â | RNA FRABASE 2.0 | RNA FRABASE 1.0 | FASTR3D |
>strand1 GAcUgAAgAuc | tRNA anticodon loop (only sequence) default options | 61 | 60 | 55 |
>strand1 GacUgAAgAuc (.........) | tRNA anticodon loop a) default options b) add through-space interactions: ON | 34 47 | 34 - | 32 - |
>strand1 NNNGNRANNN (((....))) | Hairpin GNRA loop a) default options b) include all models: ON | 2120 2125 | 1680 - | 1498 - |
>strand1 NNNGNRANNN ((?....?)) | Hairpin GNRA loop default options | 2392 | - | - |
>strand1 ^(((((((((($ >strand2 ^))))))))))$ | Decamer duplex default options | 67 | - | - |
>strand1 ^((((((( >strand2 )))))))....$ | tRNA acceptor stem default options | 143 | - | - |
>strand1 NNNANNN (((.((( >strand2 NNNNNN )))))) | Duplex with a single adenosine bulge: a) default options b) strand shift operation: ON | 356 606 | 287 - | - - |
>strand1 (......( >strand2 ).....) | Internal loop (E loop in 5S rRNA) a) default options b) strand shift operation: ON | 258 528 | 226 - | 209 - |
>strand1 ((.......(( >strand2 ))....(( >strand3 ))..)) | Three-way junction loop (in ribozyme) default options | 12 | 11 | 14 |
>strand1 (((....).(( >strand2 ))...(( >strand3 )).)) | Three-way junction loop (in hammerhead) a) default options b) strand shift operation: ON | 2 4 | 2 - | 2 - |
>strand1 (((.[[[[[[))) >strand2 (((.]]]]]]))) | Kissing loop default options | 57 | 52 | 48 |