Supplementary Material for Rna Pseudoknot Removal 1 Pseudoknot Removal by an Optimization Approach 1.1 Modification of Nussinov-jacobson Algorithm

@inproceedings{SmitSupplementaryMF,
  title={Supplementary Material for Rna Pseudoknot Removal 1 Pseudoknot Removal by an Optimization Approach 1.1 Modification of Nussinov-jacobson Algorithm},
  author={J H A De Smit}
}
The original Nussinov-Jacobson algorithm (Nussinov and Jacobson 1980) calculates an RNA secondary structure containing the maximum number of base pairs, where GC and AU base pairs are allowed (optionally GU base pairs and loop-size restrictions can be added). By restricting this algorithm to the base pairs in the knotted structure it calculates a nested… CONTINUE READING