@InProceedings{Will:Busch:Backofen:_effic_const_sequen_align_clust_tree_elimin:WCB05,
  author =	 {Sebastian Will and Anke Busch and Rolf Backofen},
  title =	 {Efficient Constraint-based Sequence Alignment by Cluster
                  Tree Elimination},
  booktitle =	 {Proceedings of the Workshop on Constraint Based Methods in
                  Bioinformatics (WCB05)},
  year =	 2005,
  pages =	 {66-74},
  place =	 {Sitges, Spain},
  user =	 {will},
  publists =	 {All and Sebastian Will and Anke Busch and Rolf Backofen},
  abstract =	 {Aligning DNA and protein sequences has become a standard
                  mehtod in molecular biology. Often, it is desirable to
                  include partial prior knowledge and conditions in an
                  alignment. The most common and successful technique for
                  efficient alignment algorithms is dynamic programming
                  (DP). However, a weakness of DP is that one cannot include
                  additional constraints without specifically tailoring a new
                  DP algorithm. Here, we discuss a declarative approach that
                  is based on constraint techniques and show how it can be
                  extended by formulating additional knowledge as
                  constraints. We take special care to obtain the efficiency
                  of DP for sequence alignment. This is achieved by careful
                  modeling and applying proper solving strategies.}
}