The pixel machine: a parallel image computer
SIGGRAPH '89 Proceedings of the 16th annual conference on Computer graphics and interactive techniques
Real-time robot motion planning using rasterizing computer graphics hardware
SIGGRAPH '90 Proceedings of the 17th annual conference on Computer graphics and interactive techniques
I3D '92 Proceedings of the 1992 symposium on Interactive 3D graphics
A real-time procedural shading system for programmable graphics hardware
Proceedings of the 28th annual conference on Computer graphics and interactive techniques
Ray tracing on programmable graphics hardware
Proceedings of the 29th annual conference on Computer graphics and interactive techniques
Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware
Physically-based visual simulation on graphics hardware
Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware
Massively Parallel Solutions for Molecular Sequence Analysis
IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium
A system for interactive modeling of physical curved surface objects
SIGGRAPH '78 Proceedings of the 5th annual conference on Computer graphics and interactive techniques
Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware
Simulation of cloud dynamics on graphics hardware
Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware
A multigrid solver for boundary value problems using programmable graphics hardware
Proceedings of the ACM SIGGRAPH/EUROGRAPHICS conference on Graphics hardware
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
Nonlinear optimization framework for image-based modeling on programmable graphics hardware
ACM SIGGRAPH 2003 Papers
Fast computation of database operations using graphics processors
SIGMOD '04 Proceedings of the 2004 ACM SIGMOD international conference on Management of data
Brook for GPUs: stream computing on graphics hardware
ACM SIGGRAPH 2004 Papers
Computational biology and high-performance computing
Communications of the ACM - Bioinformatics
Space and Time Optimal Parallel Sequence Alignments
IEEE Transactions on Parallel and Distributed Systems
The UCSC Kestrel Parallel Processor
IEEE Transactions on Parallel and Distributed Systems
Merrimac: Supercomputing with Streams
Proceedings of the 2003 ACM/IEEE conference on Supercomputing
ClawHMMER: A Streaming HMMer-Search Implementatio
SC '05 Proceedings of the 2005 ACM/IEEE conference on Supercomputing
Parallel Pattern-Based Systems for Computational Biology: A Case Study
IEEE Transactions on Parallel and Distributed Systems
Bio-sequence database scanning on a GPU
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
GPU-ClustalW: using graphics hardware to accelerate multiple sequence alignment
HiPC'06 Proceedings of the 13th international conference on High Performance Computing
GPU accelerated smith-waterman
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part IV
A survey of desktop grid applications for e-science
International Journal of Web and Grid Services
A stream chip-multiprocessor for bioinformatics
ACM SIGARCH Computer Architecture News
Mars: a MapReduce framework on graphics processors
Proceedings of the 17th international conference on Parallel architectures and compilation techniques
GPU-MEME: Using Graphics Hardware to Accelerate Motif Finding in DNA Sequences
PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
High performance protein sequence database scanning on the Cell Broadband Engine
Scientific Programming - High Performance Computing with the Cell Broadband Engine
Pairwise Distance Matrix Computation for Multiple Sequence Alignment on the Cell Broadband Engine
ICCS '09 Proceedings of the 9th International Conference on Computational Science: Part I
C-based design methodology for FPGA implementation of clustalW MSA
PRIB'07 Proceedings of the 2nd IAPR international conference on Pattern recognition in bioinformatics
Molecular dynamics simulations on commodity GPUs with CUDA
HiPC'07 Proceedings of the 14th international conference on High performance computing
Parallel DNA sequence alignment on the cell broadband engine
PPAM'07 Proceedings of the 7th international conference on Parallel processing and applied mathematics
Lock-free parallel dynamic programming
Journal of Parallel and Distributed Computing
GPU-based FFT computation for multi-gigabit wirelessHD baseband processing
EURASIP Journal on Wireless Communications and Networking
Journal of Computational Physics
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
Parallelization of pagerank on multicore processors
ICDCIT'12 Proceedings of the 8th international conference on Distributed Computing and Internet Technology
High-throughput antibody sequence alignment based on GPU computing
Proceedings of the 27th Annual ACM Symposium on Applied Computing
Proceedings of the ATIP/A*CRC Workshop on Accelerator Technologies for High-Performance Computing: Does Asia Lead the Way?
Parallel longest common subsequence using graphics hardware
EG PGV'08 Proceedings of the 8th Eurographics conference on Parallel Graphics and Visualization
A data parallel strategy for aligning multiple biological sequences on multi-core computers
Computers in Biology and Medicine
On the efficacy of GPU-integrated MPI for scientific applications
Proceedings of the 22nd international symposium on High-performance parallel and distributed computing
A memory access model for highly-threaded many-core architectures
Future Generation Computer Systems
Journal of Computational Physics
International Journal of Computational Science and Engineering
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Sequence alignment is a common and often repeated task in molecular biology. Typical alignment operations consist of finding similarities between a pair of sequences (pairwise sequence alignment) or a family of sequences (multiple sequence alignment). The need for speeding up this treatment comes from the rapid growth rate of biological sequence databases: every year their size increases by a factor 1.5 to 2. In this paper we present a new approach to high performance biological sequence alignment based on commodity PC graphics hardware. Using modern graphics processing units (GPUs) for high performance computing is facilitated by their enhanced programmability and motivated by their attractive price/performance ratio and incredible growth in speed. To derive an efficient mapping onto this type of architecture, we have reformulated dynamic programming based alignment algorithms as streaming algorithms in terms of computer graphics primitives. Our experimental results show that the GPU-based approach allows speedups of over one order of magnitude with respect to optimized CPU implementations.