Sequence alignment | Page 4

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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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Source codes

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

SW# – GPU enabled exact alignments on genome scale

Matija Korpar, Mile Sikic

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Tags: Bioinformatics, Biology, Computer science, CUDA, nVidia, nVidia GeForce GTX 560, nVidia GeForce GTX 570, nVidia GeForce GTX 690, Package, Sequence alignment, Smith-Waterman algorithm

April 23, 2013 by hgpu

CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions

Yongchao Liu, Adrianto Wirawan, Bertil Schmidt

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 680, nVidia GeForce GTX 690, Package, PTX, Sequence alignment, Smith-Waterman algorithm

April 10, 2013 by hgpu

Parallel Implementation of Dynamic Programming Algorithm Using Graphics Processing Unit

M. Khurram Rehman, M. Umer Sarwar, M. Ramzan Talib, M. Salman Mansoor, M. Bilal Sarwar

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, Matrix multiplication, nVidia, nVidia GeForce GT 525 M, nVidia GeForce GT 610 M, Sequence alignment

April 6, 2013 by hgpu

GPU-Based Cloud Service for Smith-Waterman algorithm Using Frequency Distance Filtration Scheme

Sheng-Ta Lee, Chun-Yuan Lin, Che Lun Hung

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

March 18, 2013 by hgpu

Binary Interval Search: 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, Monte Carlo simulation, nVidia, Package, Sequence alignment

February 6, 2013 by hgpu

Burrows-Wheeler Aligner: A Parallel Approach

Sheridan Lee Wright

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Tags: Algorithms, Bioinformatics, Biology, CUDA, MPI, nVidia, Sequence alignment, Thesis

January 16, 2013 by hgpu

High performance bioinformatics and computational biology on general-purpose graphics processing units

Cheng Ling

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Tags: Bioinformatics, Biology, Computational biology, CUDA, FPGA, nVidia, nVidia GeForce 8800 GTX, nVidia GeForce GTX 460, Sequence alignment, Thesis

January 3, 2013 by hgpu

GPU Acceleration of Pyrosequencing Noise Removal

Yang Gao, Jason D. Bakos

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Tags: Algorithms, Bioinformatics, Biology, Clustering, CUDA, MPI, nVidia, Sequence alignment, Tesla C2070

November 10, 2012 by hgpu

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

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

gpu_tracker: Python package for tracking and profiling GPU utilization in both desktop and high-performance computing environments

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

LOOPer: A Learned Automatic Code Optimizer For Polyhedral Compilers

OpenMC Monte Carlo Code

Performance Portable Monte Carlo Particle Transport on Intel, NVIDIA, and AMD GPUs

Polygeist: C/C++ frontend for MLIR

Retargeting and Respecializing GPU Workloads for Performance Portability

Parallel Gaussian process with kernel approximation in CUDA

Optical flow algorithms for SYCL

SYCL in the edge: performance and energy evaluation for heterogeneous acceleration

OpenMP5-Offload-OpenMC-Intel-PVC

Distributed OpenMP Offloading of OpenMC on Intel GPU MAX Accelerators

See all packages

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high performance computing on graphics processing units: hgpu.org

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

SW# – GPU enabled exact alignments on genome scale

CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions

Parallel Implementation of Dynamic Programming Algorithm Using Graphics Processing Unit

Binary Interval Search: a scalable algorithm for counting interval intersections

Burrows-Wheeler Aligner: A Parallel Approach

High performance bioinformatics and computational biology on general-purpose graphics processing units

GPU Acceleration of Pyrosequencing Noise Removal

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

Recent source codes

QArray

Celerity: High-level C++ for Accelerator Clusters

CIFAR-10 Airbench: 94% on CIFAR-10 in 3.29 second

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

OpenMC Monte Carlo Code

Polygeist: C/C++ frontend for MLIR

Parallel Gaussian process with kernel approximation in CUDA

Optical flow algorithms for SYCL

OpenMP5-Offload-OpenMC-Intel-PVC

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