Webserver for Aligning structural RNAs


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
Something went wrong in generating the consensus alignment

Cluster tree of the methods



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.