@Article{SiebertJCB07,
  author =	 {Siebert, Sven and Backofen, Rolf},
  title =	 {A dynamic programming approach for finding common patterns 
                  in {RNAs}},
  journal =	 JCB,
  year =	 {2007},
  volume =	 {14},
  number =	 {1},
  pages =	 {33-44},
  user =	 {heyne},
  pmid =	 {17381344},
  doi = 	 {10.1089/cmb.2006.0089},
  abstract =	 {We developed a dynamic programming approach of computing 
                  common sequence structure patterns among two RNAs given 
                  their primary sequences and their secondary structures. 
                  Common patterns between two RNAs are defined to share the 
                  same local sequential and structural properties. The 
                  locality is based on the connections of nucleotides given by 
                  their phosphodiester and hydrogen bonds. The idea of 
                  interpreting secondary structures as chains of structure 
                  elements leads us to develop an efficient dynamic 
                  programming approach in time O(nm) and space O(nm), where n 
                  and m are the lengths of the RNAs. The biological motivation 
                  is given by detecting common, local regions of RNAs, 
                  although they do not necessarily share global sequential and 
                  structural properties. This might happen if RNAs fold into 
                  different structures but share a lot of local, stable 
                  regions. Here, we illustrate our algorithm on Hepatitis C 
                  virus internal ribosome entry sites. Our method is useful 
                  for detecting and describing local motifs as well. An 
                  implementation in C++ is available and can be obtained by 
                  contacting one of the authors.}
}