@InProceedings{Otto:Will:Backofen:_struc_local_multip_align_of_rna:CGB08,
  author =	 {Wolfgang Otto and Sebastian Will and Rolf Backofen},
  title =	 {Structure Local Multiple Alignment of {RNA}},
  booktitle =	 {Proceedings of German Conference on Bioinformatics
                  (GCB'2008)},
  publisher =	 {Gesellschaft f{\"u}r Informatik (GI)},
  series =	 {Lecture Notes in Informatics (LNI)},
  volume =	 {P-136},
  year =	 2008,
  pages =	 {178-188},
  isbn =	 {987-3-88579-230-7},
  issn =	 {1617-5468},
  abstract =	 {Today, RNA is well known to perform important
                  regulatory and catalytical function due to its
                  distinguished structure. Consequentially, structure
                  is conserved in evolution and state-of-the art RNA
                  multiple alignment algorithms consider structure as
                  well as sequence information. However, existing
                  tools neglect the important aspect of
                  locality. Notably, locality in RNA occurs as
                  similarity of subsequences as well as similarity of
                  only substructures. <p> We present a novel approach
                  for multiple alignment of RNAs that deals with both
                  kinds of locality. The approach extends LocARNA by
                  structural locality and delegates the construction
                  of multiple alignments to T-Coffee.  <p> The paper
                  systematically investigates structural locality in
                  known RNA families. Benchmarking multiple alignment
                  tools on structurally local families shows the need
                  for algorithmic support of this locality. The
                  improvement in accuracy in special cases is achieved
                  while staying competitive with state-of-the-art
                  alignment tools across the whole Bralibase.  <p>
                  LocARNA and its T-Coffee extended variant LocARNATE
                  are freely available at
                  http://www.bioinf.uni-freiburg.de/Software/LocARNA/.},
  user =	 {will}
}