@Article{Backofen:Narayanaswamy:Swidan:Prote_simil_searc:2002,
  author =	 {Rolf Backofen and N. S. Narayanaswamy and Firas Swidan},
  title =	 {Protein similarity search under {mRNA} structural 
                  constraints: application to targeted selenocysteine 
                  insertion},
  journal =	 {In Silico Biology},
  year =	 {2002},
  volume =	 {2},
  number =	 {3},
  pages =	 {275-90},
  user =	 {will},
  annote =	 {bioinformatics},
  pmid =	 {12542413},
  abstract =	 {Selenocysteine is the 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, 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 
                  considering the hairpin-like SECIS-structure (and, more 
                  generally, when considering a structure that does not 
                  contain pseudoknots).}
}