相关论文: Solving The Longest Overlap Region Problem for Non…

Traditionally, we usually utilize the method of shotgun to cut a DNA sequence into pieces and we have to reconstruct the original DNA sequence from the pieces, those are widely used method for DNA assembly. Emerging DNA sequence…

Parallel computing can offer an enormous advantage regarding the performance for very large applications in almost any field: scientific computing, computer vision, databases, data mining, and economics. GPUs are high performance many-core…

BarraCUDA is a C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. The genetically improved (GI) code is up to three times faster on short paired end…

Analysis of DNA samples is an important step in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base…

These notes accompany the open-source code published in GitHub which implements a GPU-based line-segment, surface-triangle intersection algorithm in CUDA. It mentions some relevant works and discusses issues specific to this implementation.…

The development of multicore architectures supporting parallel data processing has led to a paradigm shift, which affects communication systems significantly. This article provides a scalable parallel approach of an iterative LDPC decoder,…

This paper presents a computationally efficient implementation of a Hamming code decoder on a graphics processing unit (GPU) to support real-time software-defined radio (SDR), which is a software alternative for realizing wireless…

CUDA is one of the most popular choices for GPU programming, but it can only be executed on NVIDIA GPUs. Executing CUDA on non-NVIDIA devices not only benefits the hardware community, but also allows data-parallel computation in…

Computational Pangenomics is an emerging field that studies genetic variation using a graph structure encompassing multiple genomes. Visualizing pangenome graphs is vital for understanding genome diversity. Yet, handling large graphs can be…

We report on our efforts to implement overlap fermions on NVIDIA GPUs using CUDA, commenting on the algorithms used, implemetation details, and the performance of our code.

Sequence alignment is a cornerstone of bioinformatics, widely used to identify similarities between DNA, RNA, and protein sequences and studying evolutionary relationships and functional properties. The Needleman-Wunsch algorithm remains a…

For the problem whether Graphic Processing Unit(GPU),the stream processor with high performance of floating-point computing is applicable to neural networks, this paper proposes the parallel recognition algorithm of Convolutional Neural…

In this paper, a contrastive evaluation of massively 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. Besides…

Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…

Sequence alignment is one of the oldest and the most famous problems in bioinformatics. Even after 45 years, for one reason or another, this problem is still actual; current solutions are trade-offs between execution time, memory…

The p-median problem is a well-known NP-hard problem. Many heuristics have been proposed in the literature for this problem. In this paper, we exploit a GPGPU parallel computing platform to present a new genetic algorithm implemented in…

We present an assignment for a full Parallel Computing course. Since 2017/2018, we have proposed a different problem each academic year to illustrate various methodologies for approaching the same computational problem using different…

DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…

Linear Programs (LPs) appear in a large number of applications and offloading them to the GPU is viable to gain performance. Existing work on offloading and solving an LP on GPU suggests that performance is gained from large sized LPs…

Efficiently solving NP-complete problems-such as protein structure prediction, cryptographic decryption, and vulnerability detection-remains a central challenge in computer science. Traditional electronic computers, constrained by the…