I am working on the acceleration of RNA folding algorithms using CUDA/GPU. Does anyone know more algorithms similar to the Nussinov's algorithm which can be accelerated using parallel programming or dynamic programming?
The following papers discuss algorithms suitable to your interest. Please have a look at them.
[1] : Optimization of an RNA folding algorithm for parallel architectures (http://www.sciencedirect.com/science/article/pii/S0167819198000544)
[2] : An RNA folding algorithm including pseudoknots based on dynamic weighted matching
(http://www.sciencedirect.com/science/article/pii/S1476927105001027)
[3] : Simulating the Folding Pathway of RNA Secondary Structure Using the Modified Ant Colony Algorithm (http://www.sciencedirect.com/science/article/pii/S1672652910602703)
You can also look many more papers at sciencedirect.com.
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