@Article{Siebert:Backofen:MARNA_multi_align:2005,
  author =	 {Sven Siebert and Rolf Backofen},
  title =	 {{MARNA}: multiple alignment and consensus structure 
                  prediction of {RNAs} based on sequence structure comparisons},
  journal =	 {Bioinformatics},
  year =	 {2005},
  volume =	 {21},
  number =	 {16},
  pages =	 {3352-9},
  user =	 {siebert},
  pmid =	 {15972285},
  abstract =	 {MOTIVATION: Due to the importance of considering secondary 
                  structures in aligning functional RNAs, 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 
                  explicit structural information is missing. RESULTS: We 
                  describe a novel approach for multiple alignment of RNAs 
                  (MARNA) taking into consideration both the primary and the 
                  secondary structures. It is based on pairwise 
                  sequence-structure comparisons of RNAs. From these 
                  sequence-structure alignments, libraries of weighted 
                  alignment edges are generated. The weights reflect the 
                  sequential and structural conservation. For sequences whose 
                  secondary structures are missing, the libraries are 
                  generated by sampling low energy conformations. The 
                  libraries are then processed by the T-Coffee system, which 
                  is a consistency based multiple alignment method. 
                  Furthermore, we are able to extract a consensus-sequence and 
                  -structure from a multiple alignment. We have successfully 
                  tested MARNA on several datasets taken from the Rfam 
                  database. AVAILABILITY: MARNA can be used online on our 
                  webpage www.bio.inf.uni-jena.de/Software/MARNA/index.html }
}