high performance computing on graphics processing units: hgpu.org

hgpu.org » Sequence alignment

Accelerating the Smith-Waterman Algorithm for Bio-sequence Matching on GPU

Qianghua Zhu, Fei Xia, Guoqing Jin

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Databases, nVidia, nVidia GeForce GTX 470, Sequence alignment, Sequence matching, Smith-Waterman algorithm

September 16, 2012 by hgpu

Binary Interval Search (BITS): A Scalable Algorithm for Counting Interval Intersections

Ryan M. Layer, Kevin Skadron, Gabriel Robins, Ira M. Hall, Aaron R. Quinlan

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, nVidia, Package, Search, Sequence alignment

August 17, 2012 by hgpu

Algorithms for the mapping of genome sequences in GPGPU

David Seide

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Tags: Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 280, Sequence alignment, Thesis

August 5, 2012 by hgpu

An Algorithm for Fast Edit Distance Computation on GPUs

Reza Farivar, Harshit Kharbanda, Shivaram Venkataraman, Roy H. Campbell

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, nVidia, nVidia GeForce GTX 275, Security, Sequence alignment

March 11, 2012 by hgpu

Parallelization of Myers Fast Bit-Vector Algorithm using GPGPU

Lars Langner

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Tags: Algorithms, Computer science, CUDA, nVidia, nVidia GeForce GTX 460, OpenCL, Sequence alignment, String matching, Thesis

January 27, 2012 by hgpu

Accelerated Large-Scale Multiple Sequence Alignment

Scott Lloyd, Quinn O. Snell

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Tags: Algorithms, Bioinformatics, Biology, FPGA, Package, Sequence alignment

January 19, 2012 by hgpu

BarraCUDA – a fast short read sequence aligner using graphics processing units

Petr Klus, Simon Lam, Dag Lyberg, Ming Sin Cheung, Graham Pullan, Ian McFarlane, Giles S. H. Yeo, Brian Y. H. Lam

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Tags: Bioinformatics, Biology, CUDA, nVidia, Package, Sequence alignment, Tesla M2050, Tesla M2090

January 13, 2012 by hgpu

Accurate Sequence Alignment using Distributed Filtering on GPU Clusters

Reza Farivar, Shivaram Venkataraman, Yanen Li, Ellick Chan, Abhishek Verma, Roy H. Campbell

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Tags: Bioinformatics, Biology, CUDA, Filtering, GPU cluster, nVidia, Sequence alignment, Tesla S1070

December 26, 2011 by hgpu

Achieving High Throughput Sequencing with Graphics Processing Units

Su Chen, Chaochao Zhang, Feng Shen, Ling Bai, Hai Jiang, Damir Herman

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Tags: Algorithms, Bioinformatics, Computer science, CUDA, nVidia, Sequence alignment, Tesla C2050

December 10, 2011 by hgpu

Application of GPGPU for Acceleration of Short DNA Sequence Alignment in Unipro UGENE Project

Konstantin Okonechinkov, German Grekhov, Konstantin Stepanyuk, Mikhail Fursov

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Tags: Algorithms, Bioinformatics, Biology, nVidia, OpenCL, Package, Sequence alignment, Tesla C1060, Tesla C2070

November 22, 2011 by hgpu

Improving CUDASW++, a Parallelization of Smith-Waterman for CUDA Enabled Devices

Doug Hains, Zach Cashero, Mark Ottenberg, Wim Bohm, Sanjay Rajopadhye

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C1060, Tesla C2050

November 5, 2011 by hgpu

Parallel Computing the Longest Common Subsequence (LCS) on GPUs: Efficiency and Language Suitability

Amine Dhraief, Raik Issaoui, Abdelfettah Belghith

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 430, OpenCL, Sequence alignment

October 28, 2011 by hgpu

Large Language Model Powered C-to-CUDA Code Translation: A Novel Auto-Parallelization Framework

GigaAPI: a user-space API that simplifies multi-GPU programming, bridging the gap between the capabilities of parallel GPU systems and the ability of developers to harness their full potential

GigaAPI for GPU Parallelization

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

Advances in Semantic Patching for HPC-oriented Refactorings with Coccinelle

DuoReduce: MLIR's benchmark

Hardware-Assisted Software Testing and Debugging for Heterogeneous Computing

Shamrock: Multi-GPU hydrodynamics for astrophysics

The Shamrock code: I- Smoothed Particle Hydrodynamics on GPUs

LLMPerf: GPU Performance Modeling meets Large Language Models

Hercules: A Compiler for Productive Programming of Heterogeneous Systems

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high performance computing on graphics processing units: hgpu.org

Accelerating the Smith-Waterman Algorithm for Bio-sequence Matching on GPU

Binary Interval Search (BITS): A Scalable Algorithm for Counting Interval Intersections

Algorithms for the mapping of genome sequences in GPGPU

An Algorithm for Fast Edit Distance Computation on GPUs

Parallelization of Myers Fast Bit-Vector Algorithm using GPGPU

Accelerated Large-Scale Multiple Sequence Alignment

BarraCUDA – a fast short read sequence aligner using graphics processing units

Accurate Sequence Alignment using Distributed Filtering on GPU Clusters

Achieving High Throughput Sequencing with Graphics Processing Units

Application of GPGPU for Acceleration of Short DNA Sequence Alignment in Unipro UGENE Project

Improving CUDASW++, a Parallelization of Smith-Waterman for CUDA Enabled Devices

Parallel Computing the Longest Common Subsequence (LCS) on GPUs: Efficiency and Language Suitability

Recent source codes

Large Language Model Powered C-to-CUDA Code Translation: A Novel Auto-Parallelization Framework

GigaAPI: a user-space API that simplifies multi-GPU programming, bridging the gap between the capabilities of parallel GPU systems and the ability of developers to harness their full potential

Coccinelle: a C code transformation engine using SmPL for matches, refactorings, and bug fixing

DuoReduce: MLIR's benchmark

Shamrock: Multi-GPU hydrodynamics for astrophysics

LLMPerf: GPU Performance Modeling meets Large Language Models

Hercules: A Compiler for Productive Programming of Heterogeneous Systems

Celerity Runtime: High-level C++ for Accelerator Clusters

wgpy: WebGL accelerated numpy-compatible array library for web browser

Microbenchmarking OpenMP target offload with Catch2

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