@InProceedings{Bac:Nar:Swi:GCB01,
  author =       {Rolf Backofen and ~N.S.~Narayanaswamy and Firas
                  Swidan},
  editor    =    {Edgar Wingender},
  title =        {Protein similarity search under {mRNA} structural
                  constraints: application to selenocysteine incorporation},
  booktitle =    "Proc. of German Conference on Bioinformatics (GCB2001)",
  year =         2001,
  pages =        {135-140},
  isbn      = {3-00-008114-3},
  abstract =     {Selenocysteine is the recently found 21th amino acid,
                  which occurs in all kingdoms of life. Selenocysteine
                  is encoded by the STOP-codon UGA. For its insertion,
                  it requires a specific mRNA sequence downstream the
                  UGA-codon that forms a hairpin like structure (called
                  Sec insertion sequence (SECIS)). We consider the
                  computational problem of generating new amino acid
                  sequences containing selenocysteine. This requires to
                  find an mRNA sequence that is similar to the
                  SECIS-consensus, that is able to form the secondary
                  structure required for selenocysteine insertion,  and
                  whose translation is maximally similar to the original
                  amino acid sequence. We show that the problem can be
                  solved in  linear time when the structure does not
                  contain pseudoknots.}
}