@Article{Siebert:Backofen:Methods:2007,
  author =	 {Siebert, Sven and Backofen, Rolf},
  title =	 {Methods for multiple alignment and consensus structure 
                  prediction of {RNAs} implemented in {MARNA}},
  journal =	 {Methods Mol Biol},
  year =	 {2007},
  volume =	 {395},
  number =	 {},
  pages =	 {489-502},
  user =	 {backofen},
  pmid =	 {17993694},
  abstract =	 {Multiple alignments of RNAs are an essential prerequisite 
                  to further analyses such as homology modeling, motif 
                  description, or illustration of conserved or variable 
                  binding sites. Beyond the comparison of RNAs on the sequence 
                  level, structural conformations determined by basepairs have 
                  to be taken into account. Several pairwise 
                  sequence-structure alignment methods have been developed. 
                  They use extended alignment scores that evaluate secondary 
                  structure information in addition to sequence information. 
                  However, two problems for the multiple alignment step 
                  remain. First, how to combine pairwise sequence-structure 
                  alignments into a multiple alignment and, second, how to 
                  generate secondary structure information for sequences whose 
                  structural information is missing. Here, we describe MARNA, 
                  its underlying methods and its usage. MARNA is an approach 
                  for multiple alignment of RNAs taking into considerations 
                  both the primary sequences and the secondary structures. It 
                  relies on the pairwise sequence-structure comparison 
                  strategy by generating a set of weighted alignment edges. 
                  This set is processed by a consistency-based multiple 
                  alignment method. Additionally, MARNA extracts a 
                  consensus-sequence and structure from this generated 
                  multiple alignment. MARNA can be accessed via the 
                  http://www.bioinf.uni-freiburg.de/Software/MARNA.}
}