@inproceedings{backofensiebert:2004:gcb,
author     = {Rolf Backofen and Sven Siebert},
title      = {Fast Detection of Common Sequence Structure Patterns in {RNAs}},
booktitle  = {Symposium on String Processing and Information Retrieval
             (SPIRE 2004)}, 
series     = {Lecture Notes in Computer Science},
volume     = 3246,
publisher  = {Springer}, 
year       = 2004,
pages      = {79-92},
user       = {siebert},
abstract   = { 
  We developed a dynamic programming approach of computing common
  sequence/structure patterns between two RNAs given by their sequence
  and secondary structures. Common patterns between two RNAs are meant
  to share the same local sequential and structural properties.
  Nucleotides which are part of an RNA are linked together due to
  their phosphodiester or hydrogen bonds. These bonds describe the way
  how nucleotides are involved in patterns and thus delivers a
  bond-preserving matching definition. Based on this definition, we
  are able to compute all patterns between two RNAs in time O(nm)
  and space O(nm), where n and m are the lengths of the RNAs,
  respectively.  Our method is useful for describing and detecting
  local motifs and for detecting local regions of large RNAs although
  they do not share global similarities.},
keywords   = {RNA, local, pattern, motif}
}