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Bioinformatics and Life Sciences
Sequencing and protein docking are very compute-intensive tasks that see a large performance benefit by using a CUDA-enabled GPU. There is quite a bit of ongoing work on using GPUs for a range of Bioinformatics and life sciences codes.
With the introduction of NVIDIA Tesla Bio Workbench, it provides bio-physicists and computational chemists the tools to push the boundaries of bio-chemical research, optimizing the scientific workflow and accelerating the pace of research. Learn more.
BGI Speeds Genome Analysis with GPUs
Learn how Chinese genomics powerhouse BGI used NVIDIA Tesla GPUs to accelerate DNA sequencing.
Read other success stories.
Learn how Chinese genomics powerhouse BGI used NVIDIA Tesla GPUs to accelerate DNA sequencing.
Read other success stories.
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| Accelerating HMMER using GPUs Scalable Informatics |
MUMmerGPU: High-through DNA sequence alignment using GPUs Schatz, et al |
Key Bioinformatics ISVs and Applications using CUDA
| ISV | DESCRIPTION | GPU ADVANTAGE |
| Protein sequence database scanning using NCBI BLASTP | 10x speed-up: from minutes on CPUs to seconds on GPUs | |
| Protein sequence database (Smith-Waterman) scanning | 10x-50x speed-up: achieving up to 30 GCUPs on query lengths over 5000 | |
| HMMER accelerated on CUDA | 60-100x speed-up: from hours on CPUs to minutes on GPUs | |
| Protein-Protein interaction modeling application | 6x speed-up: superior to FPGA-based system for protein-protein docking | |
| Molecule shape comparison application | 170x speed-up: faster screening for drug discovery (see slide 43) |
Other Relevant Software using CUDA
- MUMmerGPU: High-throughput DNA sequence alignment using CUDA
- Smith-Waterman Code on GPUs
- Online CUDA Smith-Waterman
- ClustalW on CUDA: Multiple Sequence Alignment using CUDA
- Folding @ home using CUDA-enabled GPUs
- LISSOM: model of human neocortex using CUDA
- CUDA-based AutoDock from Silicon Informatics
- Sequence alignment
- MUMmerGPU: High-through DNA sequence alignment using GPUs
- CUDASW++: Smith-Waterman Sequence Database Searches
- Smith-Waterman sequence alignment using CUDA
- Papers on Bioinformatics using CUDA
- Infernal-GPU: CUDA-accelerated RNA Alignment , Infernal (INFERence of RNA Alignment)
- SWAMP Sequence alignment
- CMatch: Fast protein and gene sequence string matching
- Docking
- 3D Protein Docking
- Accelerating PIPER using CUDA
- Protein Docking work at University of Wisconsin and video interview of David Dynerman
- Jack Collins from National Cancer Institute talks about GPU computing
- High-performance computational pipeline for metagenomic data analysis
- MrBayes on GPU
- Stochastic simulation algorithm (SSA) for biological systems
- Self-organizing computation models of human visual cortex
- DNA Microarray tool for assaying gene expression by computing pairwise Euclidean distance on GPUs
- Tesla/CUDA Success stories
- Other Tesla Vertical Solutions
- CUDA Software development tools & libraries
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