Table 1.
List of software tools at http://software.ncrna.org
| Software tool | Function | Pseudo-knot | Download | Integrated web server | Stand-alone web server | |
|---|---|---|---|---|---|---|
| Max. no. of seq. | Max. length | |||||
| SCARNA | Pairwise alignment | Yes | N/A | 5 | 1000 | Yes |
| PHMMTS | Pairwise alignment (to known structure) | No | C++ source | 5 | 1000 | Yes |
| PSTAG | Pairwise alignment (to known structure) | Yes | C++ source | 5 | 70 | Yes |
| MXSCARNA | Multiple alignment | No | C++ source | 10 | 1000 | Yes |
| Murlet | Multiple alignment | No | C++ source | 5 | 300 | Yes |
| RNAmine | Motif extraction | No | contact | 10 | 500 | No |
| SOKOS/CAN | Sequence comparison | No | C source | N/A | N/A | No |
| Stem Kernel | Sequence comparison | Yes | C++ source | N/A | N/A | No |
| miRRim | miRNA finding | No | Source script | N/A | N/A | No |
| McCaskill-MEA | Common secondary structure prediction | No | C++ source | N/A | N/A | No |
| Rfold | Base pairing probabilities | No | C++ source | N/A | N/A | No |