title: Multicore and GPU Algorithms for Nussinov RNA Folding.
abstract: We develop cache efficient, multicore, and GPU algorithms for RNA folding using Nussinov's equations. Our cache efficient algorithm provides a speedup between 1.6 and 3.0 relative to a naive straightforward single core code. The multicore version of the cache efficient single core algorithm provides a speedup, relative to the naive single core algorithm, between 7.5 and 14.0 on a 6 core hyperthreaded CPU. Our GPU algorithm for the NVIDIA C2050 is up to 1582 times as fast as the naive single core algorithm and between 5.1 and 11.2 times as fast as the fastest previously known GPU algorithm for Nussinov RNA folding.
authors.affiliation: Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611.
authors.forename: Junjie
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611.
authors.forename: Sanjay
authors.initials: S
authors.lastname: Ranka
authors.affiliation: Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611.
authors.forename: Sartaj
authors.initials: S
authors.lastname: Sahni
keywords: CUDA; GPU; Nussinov’s Algorithm; RNA Folding; cache; multicore