@Article{Sorescu_Mohl_Mann-CARNA_RNA_struc-NAR2012,
  author =	 {Dragos A. Sorescu and Mathias M{\"o}hl and Martin Mann and Rolf Backofen and Sebastian Will},
  title =	 {{CARNA} - alignment of {RNA} structure ensembles},
  journal =	 {Nucleic Acids Res},
  year =	 {2012},
  volume =	 {40},
  number =	 {W1},
  pages =	 {W49-W53},
  note = 	 {DAS, MM{\"o}, and MMa contributed equally to this work.},
  user =	 {will},
  pmid =	 {22689637},
  doi = 	 {10.1093/nar/gks491},
  issn = 	 {1362-4962},
  issn = 	 {0305-1048},
  abstract =	 {Due to recent algorithmic progress, tools for the gold 
                  standard of comparative RNA analysis, namely Sankoff-style 
                  simultaneous alignment and folding, are now readily 
                  applicable. Such approaches, however, compare RNAs with 
                  respect to a simultaneously predicted, single, nested 
                  consensus structure. To make multiple alignment of RNAs 
                  available in cases, where this limitation of the standard 
                  approach is critical, we introduce a web server that 
                  provides a complete and convenient interface to the RNA 
                  structure alignment tool 'CARNA'. This tool uniquely 
                  supports RNAs with multiple conserved structures per RNA and 
                  aligns pseudoknots intrinsically; these features are highly 
                  desirable for aligning riboswitches, RNAs with conserved 
                  folding pathways, or pseudoknots. We represent structural 
                  input and output information as base pair probability dot 
                  plots; this provides large flexibility in the input, ranging 
                  from fixed structures to structure ensembles, and enables 
                  immediate visual analysis of the results. In contrast to 
                  conventional Sankoff-style approaches, 'CARNA' optimizes all 
                  structural similarities in the input simultaneously, for 
                  example across an entire RNA structure ensemble. Even 
                  compared with already costly Sankoff-style alignment, 
                  'CARNA' solves an intrinsically much harder problem by 
                  applying advanced, constraint-based, algorithmic techniques. 
                  Although 'CARNA' is specialized to the alignment of RNAs 
                  with several conserved structures, its performance on RNAs 
                  in general is on par with state-of-the-art general-purpose 
                  RNA alignment tools, as we show in a Bralibase 2.1 
                  benchmark. The web server is freely available at 
                  http://rna.informatik.uni-freiburg.de/CARNA.}
}