Speedup of RNA Pseudoknotted Secondary Structure Recurrence Computation with the Four-Russians Method

  • Yelena Frid
  • Dan Gusfield
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7402)


While secondary pseudoknotted structure prediction is computationally challenging, such structures appear to play biologically important roles in both cells and viral RNA [1]. Restricting the class of possible structures and then finding the optimal structure for that restricted class is a common method employed to deal with the computational complexity.

We derive a practical and worst-case speedup algorithm using the Four-Russians method for the O(n 6) time Rivas&Eddy Algorithm [2] describing the broadest set of structures. Fast R&E algorithm finds the optimal Rivas&Eddy fold in O(n 6/q)-time, where q ≥ log(n).

Because the solution matrix produced by Fast R&E algorithm is identical to the one produced by the original Rivas&Eddy algorithm, the contribution of the algorithm lies not only in its stand alone practicality but also in its ability to be implemented alongside heuristic speedups, leading to even greater reductions in time. Our approach is the first to achieve a Ω(log(n)) time speedup without reducing the set of possible Rivas&Eddy pseudoknotted structures. The analysis presented here of the original algorithm could be used to improve other pseudoknot algorithms with similar recurrences.


Index Point Secondary Struc Pseudoknotted Structure Compute Matrix Multiple Structural Alignment 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Yelena Frid
    • 1
  • Dan Gusfield
    • 1
  1. 1.Department of Computer ScienceU.C. DavisUSA

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