@Article{Hiller:Pudimat:Busch:Using_RNA_secon:NAR2006,
  author =	 {Hiller, Michael and Pudimat, Rainer and Busch, Anke and 
                  Backofen, Rolf},
  title =	 {Using {RNA} secondary structures to guide sequence motif 
                  finding towards single-stranded regions},
  journal =	 NAR,
  year =	 {2006},
  volume =	 {34},
  number =	 {17},
  pages =	 {e117},
  user =	 {arichter},
  pmid =	 {16987907},
  doi = 	 {10.1093/nar/gkl544},
  issn = 	 {1362-4962},
  issn = 	 {0305-1048},
  abstract =	 {RNA binding proteins recognize RNA targets in a sequence 
                  specific manner. Apart from the sequence, the secondary 
                  structure context of the binding site also affects the 
                  binding affinity. Binding sites are often located in 
                  single-stranded RNA regions and it was shown that the 
                  sequestration of a binding motif in a double-strand 
                  abolishes protein binding. Thus, it is desirable to include 
                  knowledge about RNA secondary structures when searching for 
                  the binding motif of a protein. We present the approach 
                  MEMERIS for searching sequence motifs in a set of RNA 
                  sequences and simultaneously integrating information about 
                  secondary structures. To abstract from specific structural 
                  elements, we precompute position-specific values measuring 
                  the single-strandedness of all substrings of an RNA 
                  sequence. These values are used as prior knowledge about the 
                  motif starts to guide the motif search. Extensive tests with 
                  artificial and biological data demonstrate that MEMERIS is 
                  able to identify motifs in single-stranded regions even if a 
                  stronger motif located in double-strand parts exists. The 
                  discovered motif occurrences in biological datasets mostly 
                  coincide with known protein-binding sites. This algorithm 
                  can be used for finding the binding motif of single-stranded 
                  RNA-binding proteins in SELEX or other biological sequence 
                  data.}
}