Internal loops in RNA secondary structure prediction

  title={Internal loops in RNA secondary structure prediction},
  author={Rune B. Lyngs\o and Michael Zuker and Christian N. S. Pedersen},
We present an analysis of currently used free energy functions for internal loop stability in RNA secondary structure. This analysis enables us to present an O(ls13) algorithm for evaluating internal loops thus improving the overall complexity of RNA secondary structure prediction from O(ls14) to O(ls13). Using an implementation of this algorithm we examine how reasonable a commonly used heuristic of limiting the size of internal loops evaluated has been. 
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