@inproceedings{Bac:Nar:Swi:GCB01,
author = {Backofen, Rolf and Narayanaswamy, N. S. and
          Firas, Swidan},
title = {Protein similarity search under {mRNA} structural
         constraints: application to selenocysteine incorporation},
booktitle = {Proc. of German Conference on Bioinformatics (GCB2001)},
year = {2001},
doi = {https://content.iospress.com/articles/in-silico-biology/isb00049},
pages = {135-140},
isbn = {3-00-008114-3},
editor = {Edgar Wingender},
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.}
}