Abstract
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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Nussinov, R., Pieczenik, G., Griggs, J.R., Kleitman, D.J.: Algorithm for Loop Matching. SIAM Journal on Applied Mathematics 35(1), 68–82 (1978)
NVIDIA.: CUDA C Best Practices Guide, Version 3.2. (August 2010)
NVIDIA.: CUDA C Programming Guide, Version 3.2. (October 2010)
Ponty, Y., Termier, M., Denise, A.: GenRGenS: software for generating random genomic sequences and structures. Bioinformatics 22(12), 1534–1535 (2006)
Yan, Y., Grossman, M., Sarkar, V.: JCUDA: A Programmer-Friendly Interface for Accelerating Java Programs with CUDA. In: Sips, H., Epema, D., Lin, H.-X. (eds.) Euro-Par 2009. LNCS, vol. 5704, pp. 887–899. Springer, Heidelberg (2009)
Fontana, W., Stadler, P.F., Bornberg-Bauer, E.G., Griesmacher, T., Hofacker, I.L., Tacker, M., Tarazona, P., Weinberger, E.D., Schuster, P.: RNA folding and combinatory landscapes. Phys. Rev. E 47(3), 2083–2099 (1993)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag GmbH Berlin Heidelberg
About this paper
Cite this paper
Stojanovski, M.Z., Gjorgjevikj, D., Madjarov, G. (2012). Parallelization of Dynamic Programming in Nussinov RNA Folding Algorithm on the CUDA GPU. In: Kocarev, L. (eds) ICT Innovations 2011. ICT Innovations 2011. Advances in Intelligent and Soft Computing, vol 150. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28664-3_26
Download citation
DOI: https://doi.org/10.1007/978-3-642-28664-3_26
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-28663-6
Online ISBN: 978-3-642-28664-3
eBook Packages: EngineeringEngineering (R0)