Parallelization of dynamic programming in Nussinov RNA folding algorithm on the CUDA GPU

Advances in Intelligent and Soft Computing

Volumn 150 AISC, Issue , 2012, Pages 279-289

  Stojanovski, Marina Zaharieva ^a   Gjorgjevikj, Dejan ^b   Madjarov, Gjorgji ^b  

^a UNIVERSITY OF TWENTE   (Netherlands)

^b SS CYRIL AND METHODIUS UNIVERSITY   (Macedonia)

Author keywords

[No Author keywords available]

Indexed keywords

DYNAMIC PROGRAMMING ALGORITHM; GPU PROGRAMMING; GRAPHIC CARDS; NUSSINOV ALGORITHMS; PARALLELIZATIONS; PRIMARY SEQUENCES; RNA FOLDING; RNA SECONDARY STRUCTURE PREDICTION; RNA SECONDARY STRUCTURES;

DYNAMIC PROGRAMMING; INFORMATION TECHNOLOGY; RNA; SMART CARDS;

ALGORITHMS;

EID: 84864293064     PISSN: 18675662     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-642-28664-3_26     Document Type: Conference Paper

References (6)

1. Nussinov, R., Pieczenik, G., Griggs, J.R., Kleitman, D.J.: Algorithm for Loop Matching. SIAM Journal on Applied Mathematics 35(1), 68-82 (1978)
2. NVIDIA.: CUDA C Best Practices Guide, Version 3.2. (August 2010)
3. NVIDIA.: CUDA C Programming Guide, Version 3.2. (October 2010)
4. Ponty, Y., Termier, M., Denise, A.: GenRGenS: software for generating random genomic sequences and structures. Bioinformatics 22(12), 1534-1535 (2006)
5. 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)
6. 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)