Webserver for Aligning structural RNAs
Results
Performance Table
Program ![]() | CPU time ![]() | Seq ID ![]() | Free energy ![]() | Covar. ![]() | Bp. prob. ![]() | Canonical bp. ![]() |
---|---|---|---|---|---|---|
Consensus | 0.00 | 0.26 | -15.66 | 0.95 | 0.80 | 0.00 |
CMfinder | 13.74 | 0.29 | -2.72 | 0.18 | 0.43 | 0.00 |
FoldalignM | 128.94 | 0.27 | -27.31 | 0.89 | 0.78 | 0.00 |
LaRA | 492.00 | 0.26 | -17.62 | 0.87 | 0.79 | 0.00 |
Either LocARNA was not chosen or it finished abnormally | ||||||
MASTR | 271.63 | 0.30 | 2.78 | 0.22 | 0.33 | 0.00 |
Either MXSCARNA was not chosen or it finished abnormally | ||||||
Either Murlet was not chosen or it finished abnormally | ||||||
RNASampler | 591.86 | 0.26 | -31.65 | 0.59 | 0.67 | 0.00 |
RNAforester | 1.03 | 0.25 | -17.81 | 0.33 | 0.61 | 0.00 |
Either PETfold was not chosen or it finished abnormally | ||||||
Either ClustalW + Pfold was not chosen or it finished abnormally | ||||||
RNAalifold | 0.21 | 0.29 | 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
![Tree](https://rth.dk/resources/war/webstatic/war_DUDA31/method_tree.png)
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.