Internal loops in RNA secondary structure prediction

著者: Rune B. Lyngsø, Michael Zuker, Christian N. S. Pedersen - Proceedings of the third annual international conference on Computational molecular biology 1999 被引用: 47

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(|s|³) algorithm for evaluating internal loops thus improving the overall complexity of RNA secondary structure prediction from O(|s|^4) to O(|s|³). Using an implementation of this algorithm we examine how reasonable a commonly used heuristic of limiting the size of internal loops evaluated has been.