high performance computing on graphics processing units: hgpu.org

hgpu.org » Sequence alignment

Efficient all-against-all protein similarity matrix computation using OpenCL

U. Köhler, A. Smirnov

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Tags: AMD Radeon HD 580, Bioinformatics, nVidia, OpenCL, Sequence alignment, Smith-Waterman algorithm

June 9, 2014 by hgpu

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

Andrea Manconi, Alessandro Orro, Emanuele Manca, Giuliano Armano, Luciano Milanesi

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Tags: Bioinformatics, Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 480, Package, Python, Sequence alignment, Tesla K10, Tesla K20

May 25, 2014 by hgpu

cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on a GPU

Jing Zhang, Hao Wang, Heshan Lin, Wu-chun Feng

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Tags: Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Sequence alignment, Tesla K20

May 23, 2014 by hgpu

Local Alignment Tool Based on Hadoop Framework and GPU Architecture

Che-Lun Hun, Guan-Jie Hua

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Tags: Biology, Cloud, CUDA, Hadoop, MapReduce, nVidia, nVidia GeForce GTS 480, Sequence alignment

April 19, 2014 by hgpu

Pairwise Sequence Alignment for Very Long Sequences on GPUs

J. Li, S. Ranka, S. Sahni

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Tags: CUDA, Genetics, nVidia, nVidia Tesla C2050, Sequence alignment, Smith-Waterman algorithm

April 2, 2014 by hgpu

Hybrid Framework for pairwise DNA Sequence Alignment Using the CUDA compatible GPU

H. Khaled, R. El Gohary, N.L. Badr, H. M. Faheem

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 540 M, Sequence alignment, Smith-Waterman algorithm

March 6, 2014 by hgpu

QuickProbs – A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors

Adam Gudys, Sebastian Deorowicz

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Tags: ATI, ATI Radeon HD 7970, Bioinformatics, Biology, nVidia, nVidia GeForce GTX 480, nVidia GeForce GTX 580, nVidia GeForce GTX 680, OpenCL, Package, Sequence alignment

March 4, 2014 by hgpu

Achieving TeraCUPS on Longest Common Subsequence Problem using GPGPUs

Adnan Ozsoy, Arun Chauhan, Martin Swany

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Tags: Algorithms, Computer science, CUDA, Heterogeneous systems, nVidia, nVidia GeForce GTX 480, nVidia GeForce GTX 690, Sequence alignment, Sequence matching, Tesla C2075, Tesla M2090

January 2, 2014 by hgpu

HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads

Pinghao Li, Xiaoqian Jiang, Shuang Wang, Jihoon Kim, Hongkai Xiong, Lucila Ohno-Machado

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Tags: Algorithms, Bioinformatics, Biology, Clustering, Compression, CUDA, nVidia, Package, Sequence alignment, Tesla M2090

December 27, 2013 by hgpu

Accelerating Pairwise DNA Sequence Alignment using the CUDA Compatible GPU

H. Khaled, R. El Gohary, N. L. Badr, H. M. Faheem

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Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GT 540 M, Sequence alignment, Smith-Waterman algorithm

December 22, 2013 by hgpu

GPU Multiple Sequence Alignment Fourier-Space Cross-Correlation Alignment

Matthias Alexander Lee

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Tags: Bioinformatics, Biology, Computational Complexity, CUDA, nVidia, Package, Python, RNA, Sequence alignment, Signal processing

May 31, 2013 by hgpu

A Distributed CPU-GPU Framework for Pairwise Alignments on Large-Scale Sequence Datasets

Da Li, Kittisak Sajjapongse, Huan Truong, Gavin Conant, Michela Becchi

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Tags: Bioinformatics, Biology, Computational biology, CUDA, GPU cluster, Heterogeneous systems, MPI, nVidia, nVidia Quadro FX 2000, Sequence alignment, Tesla K20

May 11, 2013 by hgpu

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Octo-Tiger: Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees

Stellar Mergers with HPX-Kokkos and SYCL: Methods of using an Asynchronous Many-Task Runtime System with SYCL

BAT: A standardized benchmark suite for auto-tuners

Towards a Benchmarking Suite for Kernel Tuners

BenchDirect: A Directed Language Model for Compiler Benchmarks

A Deep Learning Model for Loop Interchange

Bridging Control-Centric and Data-Centric Optimization

Advanced evolutionary computation library built directly on top of PyTorch, created at NNAISENSE

EvoTorch: Scalable Evolutionary Computation in Python

See all packages

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high performance computing on graphics processing units: hgpu.org

Efficient all-against-all protein similarity matrix computation using OpenCL

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on a GPU

Pairwise Sequence Alignment for Very Long Sequences on GPUs

Hybrid Framework for pairwise DNA Sequence Alignment Using the CUDA compatible GPU

QuickProbs – A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors

Achieving TeraCUPS on Longest Common Subsequence Problem using GPGPUs

HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads

Accelerating Pairwise DNA Sequence Alignment using the CUDA Compatible GPU

GPU Multiple Sequence Alignment Fourier-Space Cross-Correlation Alignment

A Distributed CPU-GPU Framework for Pairwise Alignments on Large-Scale Sequence Datasets

Recent source codes

E2C-Sim: a simulator and workload generator for Edge-to-Cloud environments

Kernel Tuner

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gpuLik

Octo-Tiger: Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees

BAT: A standardized benchmark suite for auto-tuners

BenchDirect: A Directed Language Model for Compiler Benchmarks

A Deep Learning Model for Loop Interchange

Bridging Control-Centric and Data-Centric Optimization

Advanced evolutionary computation library built directly on top of PyTorch, created at NNAISENSE

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