Sangho Lee, Youngsok Kim, Jangwoo Kim, Jong Kim
Graphics processing units (GPUs) are important components of modern computing devices for not only graphics rendering, but also efficient parallel computations. However, their security problems are ignored despite their importance and popularity. In this paper, we first perform an in-depth security analysis on GPUs to detect security vulnerabilities. We observe that contemporary, widely-used GPUs, both […]
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Gustavo Encarnacao
Since the discovery of Deoxyribonucleic Acid (DNA) significant technological advances were made, leading to very large amounts of data gathered for analysis. The tools for this analysis however have advanced at a slower pace and have become one of the limiting factors of new discoveries in this field of research. Recently, from the 3D game […]
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Adnan Ozsoy, Arun Chauhan, Martin Swany
In this paper, we describe a novel technique to optimize longest common subsequence (LCS) algorithm for one-to-many matching problem on GPUs by transforming the computation into bit-wise operations and a post-processing step. The former can be highly optimized and achieves more than a trillion operations (cell updates) per second (CUPS)-a first for LCS algorithms. The […]
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Sampath Kumar, P. K. Baruah
GPU parallelism for real applications can achieve enormous performance gain. CPU-GPU Communication is one of the major bottlenecks that limit this performance gain. Among several libraries developed so far to optimize this communication, DyManD (Dynamically Managed Data) provides better communication optimization strategies and achieves better performance on a single GPU. Smith-Waterman is a well known […]
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Gang Liao, Qi Sun, Longfei Ma, Zhihui Qin
In this paper, a contrastive evaluation of massive parallel implementations of suffix tree and suffix array to accelerate genome sequence matching are proposed based on Intel Core i7 3770K quad-core and NVIDIA GeForce GTX680 GPU(kepler architecture). Due to the more regular execution flow of the indexed binary search algorithm, the more efficient use of the […]
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Tuan Tu Tran
Searching similarities between sequences is a fundamental operation in bioinformatics, providing insight in biological functions as well as tools for high-throughput data. There is a need to have algorithms able to process efficiently billions of sequences. To look for approximate similarities, a common heuristic is to consider short words that appear exactly in both sequences, […]
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Qianghua Zhu, Fei Xia, Guoqing Jin
Nowadays, GPU has emerged as one promising computing platform to accelerate bio-sequence analysis applications by exploiting all kinds of parallel optimization strategies. In this paper, we take a well-known algorithm in the field of pair-wise sequence alignment and database searching, the Smith-Waterman (S-W) algorithm as an example, and demonstrate approaches that fully exploit its performance […]
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Themistoklis K. Pyrgiotis, Charalampos S. Kouzinopoulos, Konstantinos G. Margaritis
One of the most significant issues of the computational biology is the multiple pattern matching for locating nucleotides and amino acid sequence patterns into biological databases. Sequential implementations for these processes have become inadequate, due to an increasing demand for more computational power. Graphic cards offer a high parallelism computational power improving the performance of […]
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Raik Issaoui, Amine Draief, Abdelfettah Belghith
Recent developments in genomic and molecular technologies produced a tremendous amount of information related to molecular biology. The management and analysis of these biological data require intensive computing power. Sequence aligning is one of the algorithmic tools in bioinformatics to look for resemblance among sequences of amino acids. The longest common subsequence (LCS) of biological […]
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M. Affan Zidan, Talal Bonny, Khaled N. Salama
Many database applications, such as sequence comparing, sequence searching, and sequence matching, etc, process large database sequences. we introduce a novel and efficient technique to improve the performance of database applications by using a Hybrid GPU/CPU platform. In particular, our technique solves the problem of the low efficiency resulting from running short-length sequences in a […]
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Sun Wei-dong, Ma Zong-min
Now high-throughput sequencing technologies can yield a huge volume of sequence data with affordable price, the explosion rate of sequence data is outpacing the performance improvement of CPU, which means trivial sequence analysis task may challenge existing serial programs running purely on CPU. This paper depicts a highly parallel sequence translation program running on a […]
Bernhard Fechner
Today, nearly every user of electronic devices is affected by threats. Computer viruses infect harmless programs and change the function of that program. One means against these threats is a virus scanner, searching for signatures of known viruses within code and/or data. In this work, we present a novel approach to on-line virus scanning and […]
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