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