high performance computing on graphics processing units: hgpu.org

hgpu.org » Smith-Waterman algorithm

Parallel Approaches for SWAMP Sequence Alignment

Shannon Steinfadt, Kevin Schaffer

Tags: Bioinformatics, Biology, Cell processor, FPGA, nVidia, Sequence alignment, Smith-Waterman algorithm

April 19, 2011 by hgpu

The optimization of parallel Smith-Waterman sequence alignment using on-chip memory of GPGPU

Qian Zhang, Hong An, Gu Liu, Wenting Han, Ping Yao, Mu Xu, Xiaoqiang Li

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

April 4, 2011 by hgpu

Optimizing Smith-Waterman algorithm on Graphics Processing Unit

A. Khalafallah, H.F. Elbabb, O. Mahmoud, A. Elshamy

Tags: Bioinformatics, Biology, OpenCL, Sequence alignment, Smith-Waterman algorithm

April 1, 2011 by hgpu

Implementation of Smith-Waterman Algorithm in OpenCL for GPUs

Dzmitry Razmyslovich, Guillermo Marcus, Markus Gipp, Marc Zapatka, Andreas Szillus

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 260, nVidia GeForce GTX 480, OpenCL, Poster, Sequence alignment, Smith-Waterman algorithm

March 31, 2011 by hgpu

CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences

Edans Flavius O. Sandes, Alba Cristina M.A. de Melo

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Sequence alignment, Smith-Waterman algorithm

February 27, 2011 by hgpu

CBESW: sequence alignment on the Playstation 3

Adrianto Wirawan, Chee Keong K. Kwoh, Nim Tri T. Hieu, Bertil Schmidt

View

Download (PDF)

Source codes

Tags: Algorithms, Bioinformatics, Biology, BLAST, Cell processor, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Playstation, Sequence alignment, Smith-Waterman algorithm

January 8, 2011 by hgpu

A parameterisable and scalable Smith-Waterman algorithm implementation on CUDA-compatible GPUs

Cheng Ling, Khaled Benkrid, Tsuyoshi Hamada

View

Download (PDF)

Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Sequence alignment, Smith-Waterman algorithm

January 4, 2011 by hgpu

Design and implementation of the Smith-Waterman algorithm on the CUDA-compatible GPU

Yuma Munekawa, Fumihiko Ino, Kenichi Hagihara

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Smith-Waterman algorithm

December 22, 2010 by hgpu

A New Parallel Method of Smith-Waterman Algorithm on a Heterogeneous Platform

Bo Chen, Yun Xu, Jiaoyun Yang, Haitao Jiang

View

Download (PDF)

Tags: Biology, CUDA, nVidia, nVidia GeForce 9800 GT, Sequence alignment, Smith-Waterman algorithm

December 17, 2010 by hgpu

Scalable and highly parallel implementation of Smith-Waterman on graphics processing unit using CUDA

Ali Akoglu, Gregory Striemer

Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C870

December 15, 2010 by hgpu

SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2

Adam Szalkowski, Christian Ledergerber, Philipp Kraehenbuehl, Christophe Dessimoz

View

Download (PDF)

Source codes

Tags: Biology, Cell processor, CUDA, nVidia, nVidia GeForce 8800 GTX, Optimization, Package, Sequence alignment, Smith-Waterman algorithm

December 12, 2010 by hgpu

Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA

Yongchao Liu, Bertil Schmidt, Douglas L. Maskell

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Sequence alignment, Smith-Waterman algorithm

November 27, 2010 by hgpu

SimSYCL: Synchronous, single-threaded, library-only SYCL implementation for debugging and verification

SimSYCL: A SYCL Implementation Targeting Development, Debugging, Simulation and Conformance

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

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

94% on CIFAR-10 in 3.29 Seconds on a Single GPU

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

See all packages

* * *

high performance computing on graphics processing units: hgpu.org

Parallel Approaches for SWAMP Sequence Alignment

The optimization of parallel Smith-Waterman sequence alignment using on-chip memory of GPGPU

Optimizing Smith-Waterman algorithm on Graphics Processing Unit

Implementation of Smith-Waterman Algorithm in OpenCL for GPUs

CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences

CBESW: sequence alignment on the Playstation 3

A parameterisable and scalable Smith-Waterman algorithm implementation on CUDA-compatible GPUs

Design and implementation of the Smith-Waterman algorithm on the CUDA-compatible GPU

A New Parallel Method of Smith-Waterman Algorithm on a Heterogeneous Platform

Scalable and highly parallel implementation of Smith-Waterman on graphics processing unit using CUDA

SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2

Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA

Recent source codes

SimSYCL: Synchronous, single-threaded, library-only SYCL implementation for debugging and verification

GPU plugin for PySCF

QArray

Celerity: High-level C++ for Accelerator Clusters

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

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

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

Most viewed papers (last 30 days)