Cargando…

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

BACKGROUND: The maximal sensitivity for local alignments makes the Smith-Waterman algorithm a popular choice for protein sequence database search based on pairwise alignment. However, the algorithm is compute-intensive due to a quadratic time complexity. Corresponding runtimes are further compounded...

Descripción completa

Detalles Bibliográficos
Autores principales:	Liu, Yongchao, Wirawan, Adrianto, Schmidt, Bertil
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2013
Materias:	Methodology Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3637623/ https://www.ncbi.nlm.nih.gov/pubmed/23557111 http://dx.doi.org/10.1186/1471-2105-14-117

Ejemplares similares

CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions
por: Liu, Yongchao, et al.
Publicado: (2010)

CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units
por: Liu, Yongchao, et al.
Publicado: (2009)

Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation
por: Rognes, Torbjørn
Publicado: (2011)

Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System
por: Liu, Yu, et al.
Publicado: (2015)

SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications
por: Zhao, Mengyao, et al.
Publicado: (2013)

CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment
por: Manavski, Svetlin A, et al.
Publicado: (2008)

160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)
por: Li, Isaac TS, et al.
Publicado: (2007)

Accelerating the Smith-Waterman algorithm with interpair pruning and band optimization for the all-pairs comparison of base sequences
por: Okada, Daiki, et al.
Publicado: (2015)

GPU-Based Cloud Service for Smith-Waterman Algorithm Using Frequency Distance Filtration Scheme
por: Lee, Sheng-Ta, et al.
Publicado: (2013)

Smith-Waterman peak alignment for comprehensive two-dimensional gas chromatography-mass spectrometry
por: Kim, Seongho, et al.
Publicado: (2011)

Proposal of Smith-Waterman algorithm on FPGA to accelerate the forward and backtracking steps
por: de Oliveira, Fabio F., et al.
Publicado: (2022)

HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data
por: Wirawan, Adrianto, et al.
Publicado: (2014)

A Review of Parallel Implementations for the Smith–Waterman Algorithm
por: Xia, Zeyu, et al.
Publicado: (2021)

Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs
por: Huang, Liang-Tsung, et al.
Publicado: (2015)

Review of CPU and GPU Faddeeva Implementations
por: Oeftiger, Adrian, et al.
Publicado: (2016)

Running prototype of USolids using SIMD instructions
por: Cosmo, G.
Publicado: (2017)

Power efficiency of HEP applications on CPU & GPU
por: Tuteja, Keshvi
Publicado: (2023)

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman
por: Petti, Samantha, et al.
Publicado: (2022)

CLOVE: classification of genomic fusions into structural variation events
por: Schröder, Jan, et al.
Publicado: (2017)

CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction applications
por: Lei, Guoqing, et al.
Publicado: (2012)

Accelerating Spaceborne SAR Imaging Using Multiple CPU/GPU Deep Collaborative Computing
por: Zhang, Fan, et al.
Publicado: (2016)

Accelerating Spatial Cross-Matching on CPU-GPU Hybrid Platform With CUDA and OpenACC
por: Baig, Furqan, et al.
Publicado: (2020)

SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences
por: Rucci, Enzo, et al.
Publicado: (2018)

Cache-Oblivious parallel SIMD Viterbi decoding for sequence search in HMMER
por: Ferreira, Miguel, et al.
Publicado: (2014)

A Hybrid CPU-GPU Accelerated Framework for Fast Mapping of High-Resolution Human Brain Connectome
por: Wang, Yu, et al.
Publicado: (2013)

CPU-GPU hybrid platform for efficient spiking neural-network simulation
por: Naveros, Francisco, et al.
Publicado: (2013)

Toward Optimal Computation of Ultrasound Image Reconstruction Using CPU and GPU
por: Techavipoo, Udomchai, et al.
Publicado: (2016)

Faster dense deformable image registration by utilizing both CPU and GPU
por: Ekström, Simon, et al.
Publicado: (2021)

MIMO Radar Parallel Simulation System Based on CPU/GPU Architecture
por: Liu, Gaogao, et al.
Publicado: (2022)

SIMD Algorithms
por: Parkinson, D
Publicado: (1992)

Correction: A Hybrid CPU-GPU Accelerated Framework for Fast Mapping of High-Resolution Human Brain Connectome
por: Wang, Yu, et al.
Publicado: (2013)

A Comparison of CPU and GPU implementations for the LHCb Experiment Run 3 Trigger
por: Aaij, R., et al.
Publicado: (2021)

Fast parallel image registration on CPU and GPU for diagnostic classification of Alzheimer's disease
por: Shamonin, Denis P., et al.
Publicado: (2014)

A Hybrid CPU/GPU Pattern-Matching Algorithm for Deep Packet Inspection
por: Lee, Chun-Liang, et al.
Publicado: (2015)

Performance data of multiple-precision scalar and vector BLAS operations on CPU and GPU
por: Isupov, Konstantin
Publicado: (2020)

Digital blood in massively parallel CPU/GPU systems for the study of platelet transport
por: Kotsalos, Christos, et al.
Publicado: (2021)

Comparison of CPU and GPU bayesian estimates of fibre orientations from diffusion MRI
por: Kim, Danny H. C., et al.
Publicado: (2022)

Efficient estimation of bounded gradient-drift diffusion models for affect on CPU and GPU
por: Loossens, Tim, et al.
Publicado: (2021)

Comparing the Speed and Accuracy of the Smith and Waterman Algorithm as Implemented by Mpsrch with the Blast and Fasta Heuristics for Sequence Similarity Searching
por: Muratet, Michael A.
Publicado: (2002)

SIMD Processor Arrays
por: Parkinson, D
Publicado: (1992)

Cannot write session to /tmp/vufind_sessions/sess_73kjd7besokc017k4s09habpv8