high performance computing on graphics processing units: hgpu.org

hgpu.org » Sequence alignment

Parallelization of Myers Fast Bit-Vector Algorithm using GPGPU

Lars Langner

View

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

View

Download (PDF)

Source codes

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

View

Download (PDF)

Source codes

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

View

Download (PDF)

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

View

Download (PDF)

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

View

Download (PDF)

Source codes

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

View

Download (PDF)

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

View

Download (PDF)

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

October 28, 2011 by hgpu

Computational Biology and Applied Bioinformatics

Heitor Silverio Lopes, Leonardo Magalhaes Cruz

View

Download (PDF)

Tags: Bioinformatics, Biology, Book, Computational biology, CUDA, nVidia, Review, Sequence alignment, Spectrometry

October 23, 2011 by hgpu

DOPA: GPU-based protein alignment using database and memory access optimizations

Laiq Hasan, Marijn Kentie, Zaid Al-Ars

View

Download (PDF)

Source codes

Tags: Algorithms, Bioinformatics, Biology, Computational Complexity, CUDA, Databases, nVidia, nVidia GeForce GTX 275, Optimization, Package, Sequence alignment, Smith-Waterman algorithm

October 21, 2011 by hgpu

Large Scale DNA Sequence Alignment and Kernel Method Implemented with GPUs

Songwen Pei, Wenhao Wang, Gang Wei, Baifeng Wu

View

Download (PDF)

Tags: Algorithms, ATI, ATI Radeon HD 4870, Bioinformatics, Biology, Brook, Sequence alignment

October 1, 2011 by hgpu

Manycore high-performance computing in bioinformatics

Jean-Stephane Varre, Bertil Schmidt, Stephane Janot, Mathieu Giraud

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, OpenCL, Review, RNA, Sequence alignment

September 26, 2011 by hgpu

* * *

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

* * *

high performance computing on graphics processing units: hgpu.org

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

Computational Biology and Applied Bioinformatics

DOPA: GPU-based protein alignment using database and memory access optimizations

Large Scale DNA Sequence Alignment and Kernel Method Implemented with GPUs

Manycore high-performance computing in bioinformatics

Recent source codes

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

Kernel Tuner

Clava: C/C++ Source-to-Source Tool based on Clang

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

Most viewed papers (last 30 days)