@InProceedings{SiebertGCB03,
  author =	 {Sven Siebert and Rolf Backofen},
  title =	 {{MARNA}: A Server for Multiple Alignment of {RNAs}},
  booktitle =	 GCB,
  pages =        {135-140},
  abstract =	 {We describe an algorithmic method for multiple
                  alignment of RNAs taking into consideration both the
                  primary sequence and the secondary structure. In a
                  first step, alignment edges between nucleotides are
                  produced by pairwise sequence/structure comparisons
                  of RNAs. They are weighted with similarity scores
                  transformed from edit distances as proposed by
                  Zhang. In a next step, the set of alignment edges
                  are given as input to the multiple alignment program
                  T-COFFEE. Here, edges that are supported by several
                  pairwise alignments are strengthened. An example of
                  tRNA sequences from the Rfam database with their
                  typical cloverleaf structure is given. In addition,
                  we compare this alignment with a traditional
                  multiple sequence alignment program: clustalw. The
                  MARNA server is available at
                  http://www.bio.inf.uni-jena.de/Software/MARNA/marna.html},
  year =	 2003,
  month =	 {October},
  user =	 {siebert}
}