high performance computing on graphics processing units: hgpu.org

hgpu.org » Sequence alignment

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

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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

A tile-based parallel Viterbi algorithm for biological sequence alignment on GPU with CUDA

Zhihui Du, Zhaoming Yin, David A. Bader

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 9800 GTX, Sequence alignment

March 7, 2011 by hgpu

Efficient parallel algorithms for maximum-density segment problem

Xue Wang, Fasheng Qiu, S.K. Prasad, Guantao Chen

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Presentation, Sequence alignment

March 7, 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

Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance

Abdullah Gharaibeh, Matei Ripeanu

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Source codes

Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Sequence alignment, Short read mapping, Suffix trees

February 27, 2011 by hgpu

CBESW: sequence alignment on the Playstation 3

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

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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

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

January 4, 2011 by hgpu

Speeding up subset seed algorithm for intensive protein sequence comparison

Van Hoa Nguyen, Dominique Lavenier

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Sequence alignment

January 4, 2011 by hgpu

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

Bo Chen, Yun Xu, Jiaoyun Yang, Haitao Jiang

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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

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Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

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high performance computing on graphics processing units: hgpu.org

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

A tile-based parallel Viterbi algorithm for biological sequence alignment on GPU with CUDA

Efficient parallel algorithms for maximum-density segment problem

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

Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance

CBESW: sequence alignment on the Playstation 3

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

Speeding up subset seed algorithm for intensive protein sequence comparison

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

Recent source codes

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Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

MaC: Mamba CPU performance predictor

Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

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