Webserver for Aligning structural RNAs
Results
Performance Table
Program  | CPU time | Seq ID | Free energy | Covar. | Bp. prob. | Canonical bp. |
|---|---|---|---|---|---|---|
| Consensus | 0.00 | 0.19 | -4.24 | 0.72 | 0.72 | 0.00 |
| CMfinder | 113.73 | 0.22 | -40.93 | 0.77 | 0.79 | 0.00 |
| FoldalignM | 369.35 | 0.24 | -35.01 | 0.91 | 0.83 | 0.00 |
| LaRA | 7047.00 | 0.22 | -6.52 | 0.67 | 0.70 | 0.00 |
| Either LocARNA was not chosen or it finished abnormally | ||||||
| MASTR | 968.42 | 0.26 | 0.00 | 0.00 | 0.00 | 0.00 |
| Either MXSCARNA was not chosen or it finished abnormally | ||||||
| Either Murlet was not chosen or it finished abnormally | ||||||
| RNASampler | 20.61 | 0.24 | 0.00 | 0.00 | 0.00 | 0.00 |
| RNAforester | 3.81 | 0.21 | -11.59 | 0.25 | 0.56 | 0.00 |
| Either PETfold was not chosen or it finished abnormally | ||||||
| Either ClustalW + Pfold was not chosen or it finished abnormally | ||||||
| RNAalifold | 1.02 | 0.25 | 0.00 | 0.00 | 0.00 | 0.00 |
| Either MAFFT + Pfold was not chosen or it finished abnormally | ||||||
| Either MAFFT + RNAalifold was not chosen or it finished abnormally | ||||||
Cluster tree of the methods
| Table |
References
If you use the consensus results generated by this web server, please cite (bibtex):
Torarinsson, E. and Lindgreen, S. (2008): WAR: Webserver for aligning structural RNAs, Nucleic Acids Res., Web Server Issue, W79-84 [Link to paper]
C. Notredame, D. Higgins and J. Heringa (2000): T-Coffee: A novel method for multiple sequence alignments, J. Mol. Biol., 302(1):205-217 [Link to paper]
Z. Yao, Z. Weinberg, and W. L. Ruzzo (2006): CMfinder - a covariance model based RNA motif finding algorithm, Bioinformatics, 22(4):445-452 [Link to paper]
E. Torarinsson, J. Havgaard, and J. Gorodkin (2007): Multiple structural alignment and clustering of RNA sequences, Bioinformatics, 23(8):926-932 [Link to paper]
M. Bauer, G. W. Klau, and K. Reinert (2007): Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization, BMC Bioinformatics, 8(271) [Link to paper]
S. Lindgreen, P. Gardner, and A. Krogh (2007): MASTR: Multiple alignment and structure prediction of non-coding RNAs using simulated annealing, Bioinformatics, doi: 10.1093/bioinformatics/btm525 [Link to paper]
I. L. Hofacker, M. Fekete, and P. F. Stadler (2002): Secondary structure prediction for aligned RNA sequences, Journal of Molecular Biology, 319(5):1059-1066 [Link to paper]
J. D. Thompson, D. G. Higgins, and T. J. Gibson (1994): CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, 22(22):4673-4680 [Link to paper]
M. Höchsmann, T. Töller, R. Giegerich and S. Kurtz (2003): Local similarity of RNA secondary structures, in Proc. of the IEEE Bioinformatics Conference, 159-168 [Link to paper]
J. Reeder and R. Giegerich (2005): Consensus shapes: An alternative to the Sankoff algorithm for RNA consensus structure prediction, Bioinformatics, 21(17):3516-3523 [Link to paper]
X. Xu, Y. Ji, and G. Stormo (2007): RNA Sampler: A new sampling based algorithm for common RNA secondary structure prediction and structural alignment, Bioinformatics, 23(15):1883- 1891 [Link to paper]
If you only use the results from a single prediction please cite us (WAR) and the respective program.