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BMCBI
2010
122views more  BMCBI 2010»
13 years 8 months ago
Fast and accurate protein substructure searching with simulated annealing and GPUs
Background: Searching a database of protein structures for matches to a query structure, or occurrences of a structural motif, is an important task in structural biology and bioin...
Alex Stivala, Peter J. Stuckey, Anthony Wirth
PC
2010
177views Management» more  PC 2010»
13 years 7 months ago
Parallel graph component labelling with GPUs and CUDA
Graph component labelling, which is a subset of the general graph colouring problem, is a computationally expensive operation that is of importance in many applications and simula...
Kenneth A. Hawick, Arno Leist, Daniel P. Playne
ICMCS
2008
IEEE
208views Multimedia» more  ICMCS 2008»
14 years 3 months ago
Fast computation of general Fourier Transforms on GPUS
We present an implementation of general FFTs for graphics processing units (GPUs). Unlike most existing GPU FFT implementations, we handle both complex and real data of any size t...
Brandon Lloyd, Chas Boyd, Naga K. Govindaraju
MICRO
2010
IEEE
153views Hardware» more  MICRO 2010»
13 years 6 months ago
Throughput-Effective On-Chip Networks for Manycore Accelerators
As the number of cores and threads in manycore compute accelerators such as Graphics Processing Units (GPU) increases, so does the importance of on-chip interconnection network des...
Ali Bakhoda, John Kim, Tor M. Aamodt
BMCBI
2008
211views more  BMCBI 2008»
13 years 8 months ago
CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment
Background: Searching for similarities in protein and DNA databases has become a routine procedure in Molecular Biology. The Smith-Waterman algorithm has been available for more t...
Svetlin Manavski, Giorgio Valle