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. SPS SEN PPV MCC
Consensus0.000.40-16.700.930.560.950.890.940.940.94
CMfinder4.650.40-13.790.810.520.910.740.850.860.83
FoldalignM30.920.37-16.840.950.570.950.740.900.910.89
LaRA58.000.40-18.631.030.590.970.870.960.960.95
LocARNA7.680.41-16.220.930.630.920.840.730.960.82
MASTR170.050.42-17.220.880.580.940.860.930.940.92
MXSCARNA0.590.39-15.870.680.560.920.810.900.910.89
MURLET57.970.43-9.230.900.700.980.850.571.000.73
RNASampler96.540.37-19.381.070.590.980.820.980.980.98
RNAforester0.280.24-4.670.320.460.660.320.360.570.35
PETfold2.760.37-6.020.370.450.730.650.640.620.56
ClustalW-Pfold0.040.38-5.150.600.380.860.610.530.740.59
ClustalW-RNAalifold0.070.38-7.030.660.380.870.610.510.760.58
MAFFT-Pfold0.980.38-14.590.850.610.920.780.820.890.84
MAFFT-RNAalifold1.050.38-15.100.900.650.920.780.700.900.77

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 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]

S. Will, K. Reiche, I.L. Hofacker, P.F. Stadler and R. Backofen (2007): Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering, PLOS Comp. Bio., 3(4):e65. doi:10.1371/journal.pcbi.0030065 [Link to paper]

H. Kiryu, Y. Tabei, T. Kin and K. Asai (2007): Murlet: A practical multiple alignment tool for structural RNA sequences, Bioinformatics, 23(13):1588-1598. doi:10.1093/bioinformatics/btm146 [Link to paper]

Y. Tabei, H. Kiryu, T. Kin and K. Asai (2008): A fast structural alignment method for long RNA sequences, BMC Bioinformatics, 9(33):doi: 10.1186/1471-2105-9-33 [Link to paper]

K. Asai, H. Kiryu, M. Hamada, Y. Tabei, K. Sato, H. Matsui, Y. Sakakibara, G. Terai and T. Mituyama (2008): Software.ncrna.org: web servers for analyses of RNA sequences, Nucleic Acids Res., Web Server Issue, 36:W75-W78 [Link to paper]

D. Dalli, A. Wilm, I. Mainz and G. Steger (2006): StrAl: Progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time., Bioinformatics, 22:1593-1599 [Link to paper]

S. Seemann, J. Gorodkin, and R. Backofen (2008): Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments., Nucleic Acids Res., 36:6355-6362 [Link to paper]

B. Knudsen and J. Hein (2003): Pfold: RNA secondary structure prediction using stochastic context-free grammars, Nucleic Acids Res., 31(13):3423-3428 [Link to paper]

K. Katoh, K. Misawa, K. Kuma and T. Miyata (2002): MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Res., 30:3059-3066 [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