@InProceedings{Backofen:IDA2001,
  author =       {Rolf Backofen},
  title =        {RNA-Sequence-Structure Properties and Selenocysteine Insertion},
  booktitle =    {Proc. of the Fourth International Symposium on
                  Intelligent Data Analysis},
  year =         2001,
  pages = {187--197},
  editor=        {Frank Hoffmann and David J. Hand and Niall Adams and
                  Douglas Fisher and Gabriela Guimaraes},
  series =       {Lecture Notes in Computer Science},
  volume    = 2189,
  publisher =    {Springer Verlag},
  abstract =    {Selenocysteine (Sec) is a recently discovered 21st amino acid.
  Selenocysteine is encoded by the nucleotide triplet UGA, which is
  usually interpreted as a STOP signal. The insertion of
  selenocysteine requires an additional signal in form of a
  SECIS-element (\textbf{Se}leno\textbf{c}ysteine \textbf{I}nsertion
  \textbf{S}equence). This is an mRNA-motif, which is defined by both
  sequence-related and structure-related properties.

  The bioinformatics problem of interest is to design new selenoproteins
  (i.e., proteins containing  selenocysteine), since seleno variants of
  proteins are very useful in structure analysis. When designing
  new bacterial selenoproteins, one encounters the problem that 
  the SECIS-element itself is translated (and therefore encodes a
  subsequence of the complete protein). Hence, changes on the
  level of mRNA made in order to 
  generate a SECIS-element will also modify the amino acid
  sequence. Thus, one searches for an mRNA that is maximally similar to a
  SECIS-element, and for which the encoded amino acid sequence is
  maximally similar to the original amino acid sequence. In addition, it
  must satisfy the  constraints imposed by the structure. 

  Though the problem is NP-complete if arbitrary structural constraints are
  allowed, it can be solved efficiently when we consider the structures
  as used in SECIS-elements. The remaining 
  problem is to generate a description of the
  SECIS-element (and its diversity) based on the 
  available data.}
}