Background: The general problem of RNA secondary structure prediction under the widely used thermodynamic model is known to be NP-complete when the structures considered include arbitrary pseudoknots. For restricted classes of pseudoknots, several polynomial time algorithms have been designed, where the O(n 6 )time and O(n 4 ) space algorithm by Rivas and Eddy is currently the best available program.
Reeder and Giegerich REF improved the complexity of the algorithm, reaching the O(n 4 ) space and O(n 2 ) time, by using the Minimal Free Energy (MFE) model.
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics
BMC Bioinformatics
BMC Bioinformatics
Computer Science Medicine