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.
Consensus0.000.33-16.110.810.800.00
CMfinder2.340.3618.990.060.340.00
FoldalignM27.290.31-30.661.050.870.00
LaRA15.000.31-14.600.650.760.00
Either LocARNA was not chosen or it finished abnormally
MASTR50.840.351.980.270.470.00
Either MXSCARNA was not chosen or it finished abnormally
Either Murlet was not chosen or it finished abnormally
RNASampler10.900.35-42.990.850.870.00
RNAforester0.270.31-32.350.540.720.00
Either PETfold was not chosen or it finished abnormally
Either ClustalW + Pfold was not chosen or it finished abnormally
RNAalifold0.130.36-7.530.080.160.00
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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