A partition function algorithm for nucleic acid secondary structure including pseudoknots

@article{Dirks2003APF,
  title={A partition function algorithm for nucleic acid secondary structure including pseudoknots},
  author={Robert M. Dirks and Niles A. Pierce},
  journal={Journal of computational chemistry},
  year={2003},
  volume={24 13},
  pages={1664-77}
}
Nucleic acid secondary structure models usually exclude pseudoknots due to the difficulty of treating these nonnested structures efficiently in structure prediction and partition function algorithms. Here, the standard secondary structure energy model is extended to include the most physically relevant pseudoknots. We describe an O(N(5)) dynamic programming algorithm, where N is the length of the strand, for computing the partition function and minimum energy structure over this class of… CONTINUE READING
Highly Influential
This paper has highly influenced 31 other papers. REVIEW HIGHLY INFLUENTIAL CITATIONS
152 Extracted Citations
1 Extracted References
Similar Papers

Citing Papers

Publications influenced by this paper.
Showing 1-10 of 152 extracted citations

Referenced Papers

Publications referenced by this paper.

Studies in Foundations and Combinatorics: Advances in Mathematics Supplement Studies

  • M. S. Waterman
  • 1978

Similar Papers

Loading similar papers…