CUDA-Sankoff: Using GPU to Accelerate the Pairwise Structural RNA Alignment.
Daniel SundfeldJakob Hull HavgaardJan GorodkinAlba Cristina Magalhaes Alves de MeloPublished in: PDP (2017)
Keyphrases
- pairwise
- gpu accelerated
- sequence alignment
- rna sequences
- multiple alignment
- parallel implementation
- gpu implementation
- graphics processors
- graphics hardware
- rna secondary structures
- secondary structure
- parallel computing
- global alignment
- rna secondary structure prediction
- dna sequences
- parallel computation
- real time
- multi class
- markov random field
- protein sequences
- higher order
- genome wide
- parallel programming
- compute unified device architecture
- general purpose
- semi supervised
- free energy
- general purpose computing
- statistical significance
- graph matching
- parallel algorithm
- loss function
- similarity measure
- pairwise constraints
- pairwise interactions
- image alignment
- protein structure
- similarity function
- high throughput
- belief propagation
- graphical models
- image segmentation