Results

You can download the results in the following formats: fasta clustal stockholm col


Performance Table

Program    CPU time Seq ID Free energy Covar. Bp. prob. Canonical bp.
Consensus0.000.260.000.000.000.00
CMfinder9.730.3410.910.020.270.00
FoldalignM113.890.282.530.450.370.00
LaRA670.000.240.000.000.000.00
Either LocARNA was not chosen or it finished abnormally
MASTR354.600.300.000.000.000.00
Either MXSCARNA was not chosen or it finished abnormally
Either Murlet was not chosen or it finished abnormally
RNASampler756.290.23-11.690.430.410.00
RNAforester1.370.23-2.460.020.340.00
Either PETfold was not chosen or it finished abnormally
Either ClustalW + Pfold was not chosen or it finished abnormally
RNAalifold0.130.300.000.000.000.00
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

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 penal ties 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.












Please send any comments or report bugs to Elfar Torarinsson or Stinus Lindgreen
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