Ray tracing on programmable graphics hardware
Proceedings of the 29th annual conference on Computer graphics and interactive techniques
Massively Parallel Solutions for Molecular Sequence Analysis
IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium
Cg: a system for programming graphics hardware in a C-like language
ACM SIGGRAPH 2003 Papers
Linear algebra operators for GPU implementation of numerical algorithms
ACM SIGGRAPH 2003 Papers
The UCSC Kestrel Parallel Processor
IEEE Transactions on Parallel and Distributed Systems
Hyper customized processors for bio-sequence database scanning on FPGAs
Proceedings of the 2005 ACM/SIGDA 13th international symposium on Field-programmable gate arrays
ClawHMMER: A Streaming HMMer-Search Implementatio
SC '05 Proceedings of the 2005 ACM/IEEE conference on Supercomputing
Initial experiences porting a bioinformatics application to a graphics processor
PCI'05 Proceedings of the 10th Panhellenic conference on Advances in Informatics
Journal of VLSI Signal Processing Systems
Streaming Algorithms for Biological Sequence Alignment on GPUs
IEEE Transactions on Parallel and Distributed Systems
StoreGPU: exploiting graphics processing units to accelerate distributed storage systems
HPDC '08 Proceedings of the 17th international symposium on High performance distributed computing
GPU Accelerated RNA Folding Algorithm
ICCS '09 Proceedings of the 9th International Conference on Computational Science: Part I
On GPU's viability as a middleware accelerator
Cluster Computing
Optimizing data intensive GPGPU computations for DNA sequence alignment
Parallel Computing
Acceleration of the Smith-Waterman algorithm using single and multiple graphics processors
Journal of Computational Physics
Energy-aware high performance computing with graphic processing units
HotPower'08 Proceedings of the 2008 conference on Power aware computing and systems
GPU-ClustalW: using graphics hardware to accelerate multiple sequence alignment
HiPC'06 Proceedings of the 13th international conference on High Performance Computing
A new parallel method of smith-waterman algorithm on a heterogeneous platform
ICA3PP'10 Proceedings of the 10th international conference on Algorithms and Architectures for Parallel Processing - Volume Part I
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Speeding-up codon analysis on the cloud with local MapReduce aggregation
Information Sciences: an International Journal
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Protein sequences with unknown functionality are often compared to a set of known sequences to detect functional similarities. Efficient dynamic programming algorithms exist for this problem, however current solutions still require significant scan times. These scan time requirements are likely to become even more severe due to the rapid growth in the size of these databases. In this paper, we present a new approach to bio-sequence database scanning using computer graphics hardware to gain high performance at low cost. To derive an efficient mapping onto this type of architecture, we have reformulated the Smith-Waterman dynamic programming algorithm in terms of computer graphics primitives. Our OpenGL implementation achieves a speedup of approximately sixteen on a high-end graphics card over available straightforward and optimized CPU Smith-Waterman implementations.