Extended shapes for the combinatorial design of RNA sequences

@article{Hellmuth2009ExtendedSF,
  title={Extended shapes for the combinatorial design of RNA sequences},
  author={Marc Hellmuth and Daniel Merkle and Martin Middendorf},
  journal={International journal of computational biology and drug design},
  year={2009},
  volume={2 4},
  pages={
          371-84
        }
}
It is known that for two given secondary structures (defined by position of base pairings) an RNA string can easily be found that can fold into both structures. For more than two secondary structures this is not necessarily possible. In this paper, we introduce pseudo edges that are used to forbid that certain base pairs can bind and therefore can be used to define the properties of possible RNA secondary structures. We study the complexity of the problem to design an RNA sequence that can fold… CONTINUE READING
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