A tile-based parallel Viterbi algorithm for biological sequence alignment on GPU with CUDA.
Zhihui DuZhaoming YinDavid A. BaderPublished in: IPDPS Workshops (2010)
Keyphrases
- sequence alignment
- viterbi algorithm
- gpu accelerated
- dynamic programming
- parallel implementation
- parallel computing
- parallel programming
- parallel computation
- hidden markov models
- compute unified device architecture
- markov model
- comparative genomics
- graphics processing units
- pairwise
- shared memory
- parallel processing
- protein structure prediction
- protein sequences
- n gram
- graphics processors
- gpu implementation
- state space
- graphic processing unit
- massively parallel
- amino acids
- multiple alignment
- real time
- binding sites
- molecular biology
- multiple sequence alignment
- parallel algorithm
- natural language processing
- biological data
- conditional random fields
- language model
- general purpose
- machine learning