CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment
SA Manavski, G Valle - BMC bioinformatics, 2008 - Springer
Background Searching for similarities in protein and DNA databases has become a routine
procedure in Molecular Biology. The Smith-Waterman algorithm has been available for more …
procedure in Molecular Biology. The Smith-Waterman algorithm has been available for more …
Inter-block GPU communication via fast barrier synchronization
While GPGPU stands for general-purpose computation on graphics processing units, the
lack of explicit support for inter-block communication on the GPU arguably hampers its …
lack of explicit support for inter-block communication on the GPU arguably hampers its …
Graphics processing units and genetic programming: an overview
WB Langdon - Soft computing, 2011 - Springer
A top end graphics card (GPU) plus a suitable SIMD interpreter can deliver a several
hundred fold speed up, yet cost less than the computer holding it. We give highlights of AI …
hundred fold speed up, yet cost less than the computer holding it. We give highlights of AI …
High-throughput sequence alignment using Graphics Processing Units
Background The recent availability of new, less expensive high-throughput DNA sequencing
technologies has yielded a dramatic increase in the volume of sequence data that must be …
technologies has yielded a dramatic increase in the volume of sequence data that must be …
Streaming algorithms for biological sequence alignment on GPUs
W Liu, B Schmidt, G Voss… - IEEE transactions on …, 2007 - ieeexplore.ieee.org
Sequence alignment is a common and often repeated task in molecular biology. Typical
alignment operations consist of finding similarities between a pair of sequences (pairwise …
alignment operations consist of finding similarities between a pair of sequences (pairwise …
An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases
L Ligowski, W Rudnicki - 2009 IEEE International Symposium …, 2009 - ieeexplore.ieee.org
The Smith Waterman algorithm for sequence alignment is one of the main tools of
bioinformatics. It is used for sequence similarity searches and alignment of similar …
bioinformatics. It is used for sequence similarity searches and alignment of similar …
Acceleration of the Smith–Waterman algorithm using single and multiple graphics processors
A Khajeh-Saeed, S Poole, JB Perot - Journal of Computational Physics, 2010 - Elsevier
Finding regions of similarity between two very long data streams is a computationally
intensive problem referred to as sequence alignment. Alignment algorithms must allow for …
intensive problem referred to as sequence alignment. Alignment algorithms must allow for …
Fast detection of transformed data leaks
The leak of sensitive data on computer systems poses a serious threat to organizational
security. Statistics show that the lack of proper encryption on files and communications due …
security. Statistics show that the lack of proper encryption on files and communications due …
Optimizing data intensive GPGPU computations for DNA sequence alignment
C Trapnell, MC Schatz - Parallel computing, 2009 - Elsevier
MUMmerGPU uses highly-parallel commodity graphics processing units (GPU) to accelerate
the data-intensive computation of aligning next generation DNA sequence data to a …
the data-intensive computation of aligning next generation DNA sequence data to a …
Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming
Motivation: The introduction of next-generation sequencing techniques and especially the
high-throughput systems Solexa (Illumina Inc.) and SOLiD (ABI) made the mapping of short …
high-throughput systems Solexa (Illumina Inc.) and SOLiD (ABI) made the mapping of short …