Parallelization of Dynamic Programming in Nussinov RNA Folding Algorithm on the CUDA GPU

  • Marina Zaharieva StojanovskiEmail author
  • Dejan Gjorgjevikj
  • Gjorgji Madjarov
Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 150)


When an RNA primary sequence is folded back on itself, forming complementary base-pairs, a form called RNA secondary structure is created. The first solution for the RNA secondary structure prediction problem was the Nussinov dynamic programming algorithm developed in 1978 which is still an irreplaceable base that all other approaches rely on. In this work, the Nussinov algorithm is analyzed but from the CUDA GPU programming perspective. The algorithm is radically redesigned in order to utilize the highly parallel NUMA architecture of the GPU. The implementation of the Nussinov algorithm on CUDA architecture for NVidia GeForce 8500 GT graphic card results with substantial acceleration compared with the sequential executed algorithm.


Dynamic Program Kernel Function Shared Memory Main Diagonal Global Memory 
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 GmbH Berlin Heidelberg 2012

Authors and Affiliations

  • Marina Zaharieva Stojanovski
    • 1
    Email author
  • Dejan Gjorgjevikj
    • 2
  • Gjorgji Madjarov
    • 2
  1. 1.Formal Methods and Tools Group, Faculty EEMCSUniversity of TwenteEnschedeThe Netherland
  2. 2.Faculty of Computer Science and EngineeringSs. Cyril and Methodius UniversitySkopjeMacedonia

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