@article{lyngsø_zuker_pedersen_1999, 
  title={An Improved Algorithm for RNA Secondary Structure Prediction}, 
  DOI={10.7146/brics.v6i15.20072}, 
  abstractNote={<jats:p>Though not as abundant in known biological processes as proteins,&lt;br /&gt;RNA molecules serve as more than mere intermediaries between&lt;br /&gt;DNA and proteins, e.g. as catalytic molecules. Furthermore,&lt;br /&gt;RNA secondary structure prediction based on free energy&lt;br /&gt;rules for stacking and loop formation remains one of the few major&lt;br /&gt;breakthroughs in the field of structure prediction. We present a&lt;br /&gt;new method to evaluate all possible internal loops of size at most&lt;br /&gt;k in an RNA sequence, s, in time O(k|s|^2); this is an improvement&lt;br /&gt;from the previously used method that uses time O(k^2|s|^2).&lt;br /&gt;For unlimited loop size this improves the overall complexity of&lt;br /&gt;evaluating RNA secondary structures from O(|s|^4) to O(|s|^3) and&lt;br /&gt;the method applies equally well to finding the optimal structure&lt;br /&gt;and calculating the equilibrium partition function. We use our&lt;br /&gt;method to examine the soundness of setting k = 30, a commonly&lt;br /&gt;used heuristic.</jats:p>}, 
  number={15}, 
  publisher={Aarhus University Library}, 
  author={Lyngsø and Zuker and Pedersen}, 
  year={1999}, 
  month={Jan}
  }