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Parallelization of Dynamic Programming in Nussinov RNA Folding Algorithm on the CUDA GPU
[chapter]
2012
Advances in Intelligent and Soft Computing
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
doi:10.1007/978-3-642-28664-3_26
dblp:conf/ictinnovations/StojanovskiGM11
fatcat:de6aqtvr5bcuxcewkvjljynqfa